McCP in complex with photocaged nitric oxide, 1.44 s, 9.5 microjoule, SSX
Serial Crystallography (SX)
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 6HIH | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | BATCH MODE | | 291 | Final concentrations: 20 mg/mL protein, 50 mM HEPES pH 7.5, 34 % (v/v) polyethylene glycol 550, 500 mM MES pH 6.5, 5 mM ZnSO4. |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.95 | 58.36 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 107.183 | α = 90 |
b = 107.183 | β = 90 |
c = 107.183 | γ = 90 |
Symmetry |
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Space Group | P 21 3 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 293 | PIXEL | DECTRIS PILATUS3 6M | | 2021-09-30 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 1.00 | Diamond | I24 |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | | fixed target |
Fixed Target |
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Diffraction ID | Description | Sample Holding | Support Base | Motion control | Details | Sample Solvent |
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1 | Oxford silicon chip | | | Geobrick and Smaract | | |
Measurement |
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Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
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1 | undefined (fs) | | | undefined (KeV) | |
Data Reduction |
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Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
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1 | | | | |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | R Split (All) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot |
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1 | 2 | 75.91 | 100 | 0.992 | 0.122 | 5.8 | 63 | | 28000 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 2 | 2.03 | 100 | | 0.366 | 1.042 | 0.7 | 48.8 | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2 | 75.905 | 28000 | 1332 | 100 | 0.163 | 0.1617 | 0.1617 | 0.1942 | 0.1942 | 37.22 |
Temperature Factor Modeling |
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
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| | | | | |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_6_deg | 14.751 |
r_dihedral_angle_3_deg | 14.138 |
r_lrange_it | 9.724 |
r_scangle_it | 8.889 |
r_dihedral_angle_2_deg | 7.006 |
r_dihedral_angle_1_deg | 6.906 |
r_scbond_it | 5.826 |
r_mcangle_it | 4.487 |
r_mcbond_it | 3.347 |
r_angle_refined_deg | 2.494 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_6_deg | 14.751 |
r_dihedral_angle_3_deg | 14.138 |
r_lrange_it | 9.724 |
r_scangle_it | 8.889 |
r_dihedral_angle_2_deg | 7.006 |
r_dihedral_angle_1_deg | 6.906 |
r_scbond_it | 5.826 |
r_mcangle_it | 4.487 |
r_mcbond_it | 3.347 |
r_angle_refined_deg | 2.494 |
r_nbtor_refined | 0.317 |
r_nbd_refined | 0.21 |
r_symmetry_nbd_refined | 0.201 |
r_xyhbond_nbd_refined | 0.141 |
r_chiral_restr | 0.122 |
r_symmetry_xyhbond_nbd_refined | 0.121 |
r_gen_planes_refined | 0.011 |
r_bond_refined_d | 0.01 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 2144 |
Nucleic Acid Atoms | |
Solvent Atoms | 51 |
Heterogen Atoms | 92 |
Software
Software |
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Software Name | Purpose |
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DIALS | data reduction |
xia2 | data reduction |
xia2 | data scaling |
REFMAC | phasing |
Coot | model building |
REFMAC | refinement |