8VCW
X-Ray Crystal Structure of the biotin synthase from B. obeum
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 298 | 0.4uL protein plus 0.4 uL 100mM Bis-Tri pH 5.5, 25% PEG 3350, 0.2M NaCl equilibrated against a well of 0.5M LiCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 43.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.209 | α = 90 |
b = 50.776 | β = 90 |
c = 161.878 | 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 EIGER X 16M | mirrors | 2022-10-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-2 | 0,9793 | NSLS-II | 17-ID-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 1.35 | 80.94 | 96.9 | 0.067 | 0.076 | 0.036 | 0.998 | 12 | 4.1 | 67982 | 11.8 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.35 | 1.37 | 75 | 0.436 | 0.535 | 0.304 | 0.741 | 2.4 | 2.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FREE R-VALUE | 1.35 | 48.45 | 1.33 | 67854 | 3252 | 96.51 | 0.151 | 0.1498 | 0.1731 | Random | 12.1 |
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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 8.163 |
f_angle_d | 2.763 |
f_chiral_restr | 0.303 |
f_bond_d | 0.016 |
f_plane_restr | 0.012 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2525 |
Nucleic Acid Atoms | |
Solvent Atoms | 419 |
Heterogen Atoms | 75 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
SCALA | data scaling |
XDS | data reduction |
PHASER | phasing |