1UBL
Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.4 | 283 | MPD, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 283K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 34.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97.81 | α = 90 |
b = 125.5 | β = 90 |
c = 66.59 | 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 | CCD | MARRESEARCH | 2000-03-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44B2 | 0.700 | SPring-8 | BL44B2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.12 | 25.1 | 94.3 | 0.08 | 303804 | 297600 | 1 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.12 | 1.18 | 84.9 | 0.384 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 1H2R | 1.2 | 20 | 1 | 244116 | 189902 | 16936 | 89.1 | 0.1259 | 0.1198 | 0.1172 | 0.1611 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
298 | 7100.31 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.093 |
s_non_zero_chiral_vol | 0.091 |
s_zero_chiral_vol | 0.08 |
s_angle_d | 0.071 |
s_similar_adp_cmpnt | 0.051 |
s_anti_bump_dis_restr | 0.038 |
s_from_restr_planes | 0.0286 |
s_bond_d | 0.015 |
s_rigid_bond_adp_cmpnt | 0.006 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6196 |
Nucleic Acid Atoms | |
Solvent Atoms | 886 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
CNS | refinement |
SHELXL-97 | refinement |
CCP4 | data scaling |
CNS | phasing |