5VPW
Nitrogenase Cp1 at pH 5
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4WES |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 298 | PEG 3350, magnesium chloride, Tris/HCl, sodium dithionite |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.67 | 54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.618 | α = 90 |
b = 146.282 | β = 103.55 |
c = 116.736 | γ = 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 | 2016-05-11 | 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 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 | 1.85 | 39.2 | 98.4 | 0.079 | 11.6 | 6.5 | 189858 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.85 | 1.88 | 95.4 | 0.682 | 2.5 | 6.2 |
Refinement
Statistics | |||||||||||||||||||
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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 | 4WES | 1.85 | 39.2 | 180157 | 9635 | 98.37 | 0.16907 | 0.16738 | 0.2007 | RANDOM | 28.823 |
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] | |
-1.07 | 0.38 | 1.8 | -0.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.743 |
r_dihedral_angle_4_deg | 21.302 |
r_dihedral_angle_3_deg | 14.726 |
r_long_range_B_other | 7.753 |
r_long_range_B_refined | 7.729 |
r_scangle_other | 6.628 |
r_dihedral_angle_1_deg | 5.993 |
r_scbond_it | 4.764 |
r_scbond_other | 4.764 |
r_mcangle_it | 4.641 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14928 |
Nucleic Acid Atoms | |
Solvent Atoms | 527 |
Heterogen Atoms | 96 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data scaling |
Aimless | data scaling |
PHASER | phasing |
XDS | data reduction |