McCP in complex with photocaged nitric oxide, 1.44 s, 1600 microjoule, SSX
Serial Crystallography (SX)
Starting Model(s)
Initial Refinement Model(s) |
---|
Type | Source | Accession Code | Details |
---|
|
experimental model | PDB | 6HIH | |
Crystallization
Crystalization Experiments |
---|
ID | Method | pH | Temperature | Details |
---|
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 |
---|
Matthews coefficient | Solvent content |
---|
2.95 | 63.6 |
Crystal Data
Unit Cell |
---|
Length ( Å ) | Angle ( ˚ ) |
---|
a = 107.441 | α = 90 |
b = 107.441 | β = 90 |
c = 107.441 | γ = 90 |
Symmetry |
---|
Space Group | P 21 3 |
---|
Diffraction
Diffraction Experiment |
---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
---|
1 | 1 | x-ray | 293 | PIXEL | DECTRIS PILATUS3 6M | | 2019-12-05 | M | SINGLE WAVELENGTH |
Radiation Source |
---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
---|
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.969 | Diamond | I24 |
Serial Crystallography
Sample delivery method |
---|
Diffraction ID | Description | Sample Delivery Method |
---|
1 | Oxford silicon chip | fixed target |
Fixed Target |
---|
Diffraction ID | Description | Sample Holding | Support Base | Motion control | Details | Sample Solvent |
---|
1 | | | | Geobrick and Smaract | | |
Measurement |
---|
Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
---|
1 | undefined (fs) | | | undefined (KeV) | |
Data Reduction |
---|
Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
---|
1 | | | | |
Data Collection
Overall |
---|
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 |
---|
1 | 1.8 | 76.09 | 100 | 0.986 | 0.07 | 10.2 | 159.8 | | 38525 | | | |
Highest Resolution Shell |
---|
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) |
---|
1 | 1.8 | 1.83 | 100 | | 0.291 | 1.234 | 0.7 | 127.2 | |
Refinement
Statistics |
---|
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 |
---|
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.8 | 76.09 | 38523 | 2038 | 100 | 0.162 | 0.1605 | 0.1648 | 0.1946 | 0.1986 | 35.534 |
Temperature Factor Modeling |
---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
---|
| | | | | |
RMS Deviations |
---|
Key | Refinement Restraint Deviation |
---|
r_dihedral_angle_6_deg | 15.525 |
r_dihedral_angle_3_deg | 12.237 |
r_dihedral_angle_1_deg | 10.561 |
r_lrange_it | 10.187 |
r_scangle_it | 8.971 |
r_scbond_it | 5.953 |
r_dihedral_angle_2_deg | 5.645 |
r_mcangle_it | 4.6 |
r_mcbond_it | 3.53 |
r_angle_refined_deg | 2.514 |
RMS Deviations |
---|
Key | Refinement Restraint Deviation |
---|
r_dihedral_angle_6_deg | 15.525 |
r_dihedral_angle_3_deg | 12.237 |
r_dihedral_angle_1_deg | 10.561 |
r_lrange_it | 10.187 |
r_scangle_it | 8.971 |
r_scbond_it | 5.953 |
r_dihedral_angle_2_deg | 5.645 |
r_mcangle_it | 4.6 |
r_mcbond_it | 3.53 |
r_angle_refined_deg | 2.514 |
r_nbtor_refined | 0.313 |
r_metal_ion_refined | 0.28 |
r_nbd_refined | 0.206 |
r_symmetry_nbd_refined | 0.176 |
r_chiral_restr | 0.131 |
r_xyhbond_nbd_refined | 0.108 |
r_symmetry_xyhbond_nbd_refined | 0.06 |
r_gen_planes_refined | 0.013 |
r_bond_refined_d | 0.012 |
Non-Hydrogen Atoms Used in Refinement |
---|
Non-Hydrogen Atoms | Number |
---|
Protein Atoms | 2144 |
Nucleic Acid Atoms | |
Solvent Atoms | 88 |
Heterogen Atoms | 104 |
Software
Software |
---|
Software Name | Purpose |
---|
DIALS | data reduction |
xia2 | data reduction |
xia2 | data scaling |
MOLREP | phasing |
REFMAC | refinement |
Coot | model building |