1WUJ
Three-Dimensional Structure Of The Ni-B State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
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 |
2.33 | 47.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 98.162 | α = 90 |
b = 125.924 | β = 90 |
c = 66.441 | γ = 90 |
Symmetry | |
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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 | CCD | ADSC QUANTUM 4 | 2002-04-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL40B2 | 0.72 | SPring-8 | BL40B2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.4 | 25.21 | 99.4 | 0.069 | 161265 | 161041 | 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) | |||||||||||
1.4 | 1.48 | 97.4 | 0.376 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | 1.4 | 20 | 160944 | 139752 | 11248 | 0.125 | 0.117 | 0.115 | 0.162 | 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 |
5901 | 7063.37 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.091 |
s_zero_chiral_vol | 0.066 |
s_non_zero_chiral_vol | 0.064 |
s_anti_bump_dis_restr | 0.06 |
s_similar_adp_cmpnt | 0.047 |
s_angle_d | 0.031 |
s_from_restr_planes | 0.0284 |
s_bond_d | 0.011 |
s_rigid_bond_adp_cmpnt | 0.004 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6197 |
Nucleic Acid Atoms | |
Solvent Atoms | 834 |
Heterogen Atoms | 33 |
Software
Software | |
---|---|
Software Name | Purpose |
SHELX | model building |
SHELXL-97 | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |
CNS | phasing |