1UCQ
Crystal structure of the L intermediate of bacteriorhodopsin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1IW6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.2 | 278 | ammonium sulfate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 278.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.89 | 57.13 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 102.3 | ¦Á = 90 |
b = 102.3 | ¦Â = 90 |
c = 112.3 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 6 2 2 |
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 | 2003-02-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL40B2 | 1.0 | SPring-8 | BL40B2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.4 | 50 | 99.8 | 0.066 | 5.3 | 5.7 | 13880 | 13880 | 50.406 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.4 | 2.53 | 99.8 | 0.492 | 1.5 | 5.8 | 1986 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1iw6 | 2.4 | 50 | 14158 | 12844 | 641 | 0.3 | 0.3325 | RANDOM | 66.4738 |
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] | |
-18.641 | -11.783 | -18.641 | -37.282 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 18.20322 |
c_angle_deg | 1.27907 |
c_improper_angle_d | 0.75865 |
n_bond_d | 0.008321 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1756 |
Nucleic Acid Atoms | |
Solvent Atoms | 41 |
Heterogen Atoms | 298 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
XTALVIEW | refinement |
CNS | refinement |
CCP4 | data scaling |