DtpB in complex with photocaged nitric oxide, 10 ms, 10 microjoule, SFX
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 | 6YRJ | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | BATCH MODE | | 291 | 50 mM HEPES pH 7.5, 150 mM Magnesium chloride, 20% (w/v) PEG4000 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.63 | 53.16 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 87.073 | α = 90 |
b = 122.875 | β = 90 |
c = 194.936 | γ = 90 |
Symmetry |
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Space Group | P 21 21 21 |
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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 | 300 | CCD | RAYONIX MX-300 | | 2023-11-11 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | FREE ELECTRON LASER | SACLA BEAMLINE BL2 | 1.127 | SACLA | BL2 |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | | fixed target |
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 | 10 (fs) | 30000 | | 10.993 (KeV) | |
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 | 1.56 | 103.95 | 100 | 0.994 | 0.096 | 18.1 | 168.6 | | 295889 | | | |
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 | 1.56 | 1.59 | | | 0.316 | 1.256 | 0.9 | | |
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 (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.56 | 44.68 | 293539 | 2027 | 99.89 | 0.20891 | 0.20874 | 0.2195 | 0.23363 | 0.2437 | RANDOM | 23.355 |
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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-0.29 | | | 0.14 | | 0.15 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_3_deg | 12.268 |
r_dihedral_angle_2_deg | 8.51 |
r_long_range_B_refined | 7.509 |
r_long_range_B_other | 7.468 |
r_dihedral_angle_1_deg | 6.431 |
r_scangle_other | 5.945 |
r_scbond_it | 3.848 |
r_scbond_other | 3.837 |
r_mcangle_it | 3.545 |
r_mcangle_other | 3.545 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_3_deg | 12.268 |
r_dihedral_angle_2_deg | 8.51 |
r_long_range_B_refined | 7.509 |
r_long_range_B_other | 7.468 |
r_dihedral_angle_1_deg | 6.431 |
r_scangle_other | 5.945 |
r_scbond_it | 3.848 |
r_scbond_other | 3.837 |
r_mcangle_it | 3.545 |
r_mcangle_other | 3.545 |
r_mcbond_it | 2.418 |
r_mcbond_other | 2.417 |
r_angle_refined_deg | 1.98 |
r_angle_other_deg | 0.703 |
r_chiral_restr | 0.104 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.01 |
r_gen_planes_other | 0.006 |
r_bond_other_d | 0.001 |
r_dihedral_angle_4_deg | |
r_nbd_refined | |
r_nbd_other | |
r_nbtor_refined | |
r_nbtor_other | |
r_xyhbond_nbd_refined | |
r_xyhbond_nbd_other | |
r_metal_ion_refined | |
r_metal_ion_other | |
r_symmetry_vdw_refined | |
r_symmetry_vdw_other | |
r_symmetry_hbond_refined | |
r_symmetry_hbond_other | |
r_symmetry_metal_ion_refined | |
r_symmetry_metal_ion_other | |
r_scangle_it | |
r_rigid_bond_restr | |
r_sphericity_free | |
r_sphericity_bonded | |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 13944 |
Nucleic Acid Atoms | |
Solvent Atoms | 1102 |
Heterogen Atoms | 270 |
Software
Software |
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Software Name | Purpose |
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REFMAC | refinement |
DIALS | data scaling |
DIALS | data reduction |
PHASER | phasing |