1CP2
NITROGENASE IRON PROTEIN FROM CLOSTRIDIUM PASTEURIANUM
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1NIP | PDB ENTRY 1NIP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | liquid - liquid diffusion | 7.5 | PROTEIN WAS CRYSTALLIZED BY LIQUID-LIQUID DIFFUSION METHOD. PRECIPITANT CONTAINED 5-15% GLYCEROL, 18.75-22.5% PEG 4000, 230-270 MM CACL2, AND 50 MM HEPES PH 7.5. PROTEIN WAS STORED BEFORE CRYSTALLIZATION IN 20% GLYCEROL, 50 MM HEPES, PH 7.5, AND 2 MM NA2S2O4., liquid - liquid diffusion |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.6 | α = 90 |
b = 75.87 | β = 114.17 |
c = 53.55 | 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 | 113 | IMAGE PLATE | RIGAKU RAXIS IIC | 1993-11-25 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU |
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 | 1.93 | 15.63 | 98.8 | 0.0725 | 5.8 | 6.8 | 36808 | 34.5 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1.93 | 2 | 91 |
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 | PDB ENTRY 1NIP | 1.93 | 5 | 31231 | 3083 | 98.8 | 0.209 | 0.209 | 0.297 | RANDOM | 36.3 |
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 |
x_dihedral_angle_d | 24.1 |
x_angle_deg | 2 |
x_improper_angle_d | 1.89 |
x_bond_d | 0.018 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3940 |
Nucleic Acid Atoms | |
Solvent Atoms | 114 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
X-PLOR | model building |
X-PLOR | refinement |
R-AXIS | data reduction |
REFSTAT | data scaling |
X-PLOR | phasing |