4WES
Nitrogenase molybdenum-iron protein from Clostridium pasteurianum at 1.08 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 295 | 20% PEG 3350, 0.2 M lithium citrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.51 | 51.05 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 72.701 | ¦Á = 90 |
b = 170.581 | ¦Â = 91.63 |
c = 87.54 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | N2-cooled double focus KB mirrors | 2012-08-03 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.8856, 1.734, 1.742 | SSRL | BL12-2 |
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 | 1.08 | 38.93 | 93 | 0.064 | 9.7 | 3.6 | 842744 |
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 | 1.08 | 1.14 | 88.7 | 0.803 | 1.6 | 3.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.08 | 38.93 | 825717 | 16793 | 92.95 | 0.11088 | 0.11043 | 0.13287 | RANDOM | 16.693 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.48 | 0.45 | 0.08 | -0.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 93.667 |
r_dihedral_angle_2_deg | 35.906 |
r_sphericity_bonded | 21.493 |
r_dihedral_angle_4_deg | 19.707 |
r_dihedral_angle_3_deg | 11.868 |
r_long_range_B_refined | 11.033 |
r_long_range_B_other | 11.032 |
r_scangle_other | 8.221 |
r_scbond_it | 7.181 |
r_scbond_other | 7.181 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15133 |
Nucleic Acid Atoms | |
Solvent Atoms | 2484 |
Heterogen Atoms | 104 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |