1ML7
Crystal structure of nitrophorin 4 complexed with 4-iodopyrazole
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | ammonium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.95 | 36.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.404 | α = 90 |
b = 42.763 | β = 94.05 |
c = 52.769 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | IMAGE PLATE | MARRESEARCH | 2002-05-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | 1.080 | SSRL | BL7-1 |
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 | 1.25 | 22 | 97.8 | 0.05 | 21.7 | 5.1 | 42458 | 42458 | 7.85 |
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 | 1.25 | 1.29 | 92 | 0.158 | 7.2 | 4.7 | 3947 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | PDB entry 1IKJ | 1.25 | 20.4 | 42458 | 42458 | 2087 | 97.9 | 0.145 | 0.145 | 0.142 | 0.194 | random | 12.8 |
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 |
s_from_restr_planes | 0.1 |
s_non_zero_chiral_vol | 0.1 |
s_angle_d | 0.04 |
s_bond_d | 0.02 |
s_anti_bump_dis_restr | 0.02 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1428 |
Nucleic Acid Atoms | |
Solvent Atoms | 244 |
Heterogen Atoms | 57 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
CrystalClear | data reduction |
SHELXS | phasing |
SHELXL-97 | refinement |
CrystalClear | data scaling |