6M2E
Sirohydrochlorin nickelochelatase CfbA in complex with sirohydrochlorin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2XWS |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 293 | 0.1M ammonium sulfate, 0.3M Na-formate, 0.1M Na-acetate, 3% (w/v) gamma-PGA, 5% (w/v) PEG 3350 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.95 | 58.27 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 69.14 | α = 90 |
b = 69.14 | β = 90 |
c = 81.65 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 41 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2019-07-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 1.606990 | SPring-8 | BL44XU |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 2.6 | 48.89 | 100 | 0.059 | 0.061 | 0.999 | 25.66 | 13.665 | 11899 | 83.4 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.6 | 2.7 | 100 | 0.945 | 0.983 | 0.84 | 3.01 | 13.361 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2XWS | 2.6 | 48.89 | 11303 | 595 | 99.96 | 0.1945 | 0.1925 | 0.2348 | RANDOM | 82.477 |
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] | |
0.01 | 0.01 | -0.02 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.794 |
r_dihedral_angle_3_deg | 24.751 |
r_dihedral_angle_4_deg | 22.917 |
r_dihedral_angle_1_deg | 6.038 |
r_angle_refined_deg | 2.131 |
r_chiral_restr | 0.142 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1886 |
Nucleic Acid Atoms | |
Solvent Atoms | 5 |
Heterogen Atoms | 62 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
MOLREP | phasing |