5D40
Crystal structure of the 5-selective H176Y mutant of Cytochrome TxtE
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 295 | 25% PEG 3350, 200mM MgCl2, 100mM Bis-Tris pH 5.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.87 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.721 | α = 90 |
b = 99.207 | β = 90 |
c = 105.294 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2015-02-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.9795 | SSRL | BL12-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (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 | 1.15 | 72.206 | 97.5 | 0.1 | 0.113 | 0.052 | 8 | 4.7 | 120407 | 120407 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.51 | 1.59 | 85.4 | 0.601 | 0.601 | 0.338 | 1.1 | 4 | 15251 |
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 | 4TPN | 1.51 | 72.206 | 114245 | 6063 | 97.37 | 0.1525 | 0.1492 | 0.2153 | RANDOM | 13.754 |
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] | |
0.7 | 0.05 | -0.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 34.051 |
r_sphericity_bonded | 9.656 |
r_rigid_bond_restr | 3.929 |
r_mcangle_it | 2.133 |
r_angle_refined_deg | 1.859 |
r_mcbond_it | 1.794 |
r_mcbond_other | 1.794 |
r_angle_other_deg | 0.931 |
r_chiral_restr | 0.145 |
r_bond_refined_d | 0.019 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6284 |
Nucleic Acid Atoms | |
Solvent Atoms | 1155 |
Heterogen Atoms | 171 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |