5OG9
The BM3 mutant WIFI-WC heme domain in complex with testosterone
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1JPZ |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 297 | 25% w/v PEG 550 MME, 0.1 M MES pH 6.5, 0.01 M zinc sulfate heptahydrate |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.4 | 48.79 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 67.39 | α = 90 |
b = 89.502 | β = 90 |
c = 172.55 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
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 PILATUS3 R CdTe 300K-W | 2015-11-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.979 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.09 | 29.64 | 99 | 0.075 | 0.999 | 14.7 | 6.7 | 62142 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.09 | 2.14 | 97.3 | 0.731 | 0.786 | 2.4 | 6.7 |
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 | 1JPZ | 2.09 | 29.64 | 58933 | 3155 | 98.83 | 0.19504 | 0.19263 | 0.23865 | RANDOM | 44.692 |
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] | |
-0.05 | -0.06 | 0.11 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.541 |
r_dihedral_angle_3_deg | 16.793 |
r_dihedral_angle_4_deg | 14.064 |
r_dihedral_angle_1_deg | 6.225 |
r_angle_refined_deg | 1.768 |
r_angle_other_deg | 1.164 |
r_chiral_restr | 0.122 |
r_bond_refined_d | 0.015 |
r_gen_planes_refined | 0.009 |
r_gen_planes_other | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 7309 |
Nucleic Acid Atoms | |
Solvent Atoms | 468 |
Heterogen Atoms | 172 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
xia2 | data scaling |
Coot | model building |