2NVH
Determination of Solvent Content in Cavities in Interleukin-1 Using Experimentally-Phased Electron Density
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5I1B | PDB ENTRY 5I1B |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 7.5 | 298 | Well solution of 2.2 - 2.8 M ammonium sulfate, 100 mM Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.50 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.22 | 61.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.506 | α = 90 |
b = 54.506 | β = 90 |
c = 75.359 | γ = 90 |
Symmetry | |
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Space Group | P 43 |
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 | CCD | ADSC QUANTUM 4 | 1999-07-10 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | |||||||||||||
3 | 1 | |||||||||||||
4 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | SSRL | BL9-2 |
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 | 1.5 | 27.2 | 99.9 | 0.04 | 64 | 9.1 | 35259 | 19.5 |
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) | |||||||||||
1.5 | 1.55 | 100 | 0.298 | 8.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | NONE | PDB ENTRY 5I1B | 1.53 | 27.2 | 35287 | 35225 | 100 | 0.211 | 0.211 |
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 | |
---|---|
Key | Refinement Restraint Deviation |
t_dihedral_angle_d | 18.684 |
t_it | 14.285 |
t_angle_deg | 2.946 |
t_nbd | 0.039 |
t_bond_d | 0.025 |
t_gen_planes | 0.021 |
t_trig_c_planes | 0.012 |
t_incorr_chiral_ct | |
t_pseud_angle |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1224 |
Nucleic Acid Atoms | |
Solvent Atoms | 149 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SHARP | phasing |
TNT | refinement |
PDB_EXTRACT | data extraction |
EPMR | phasing |