2Z73
Crystal structure of squid rhodopsin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GZM | PDB ENTRY 1GZM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.4 | 277 | 3M ammonium sulfate, 30mM MES, 30mM EDTA, 10mM beta-mercaptoethanol, pH6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.45 | 64.34 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 122.55 | ¦Á = 90 |
b = 122.55 | ¦Â = 90 |
c = 158.74 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 62 |
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 | 90 | CCD | RIGAKU JUPITER 210 | 2007-05-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL38B1 | 1 | SPring-8 | BL38B1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.5 | 57 | 99.2 | 0.068 | 0.068 | 14.7 | 3.9 | 46274 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.5 | 2.64 | 0.677 | 0.495 | 1.8 | 3.8 | 6771 |
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 1GZM | 2.5 | 15 | 43279 | 2161 | 92.2 | 0.188 | 0.188 | 0.206 | RANDOM | 60.77 |
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] | |
-0.144 | -1.1 | -0.144 | 0.288 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 19.3 |
c_scangle_it | 3.17 |
c_mcangle_it | 2.66 |
c_scbond_it | 2.41 |
c_mcbond_it | 1.66 |
c_angle_deg | 1.18 |
c_improper_angle_d | 0.84 |
c_bond_d | 0.007 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5542 |
Nucleic Acid Atoms | |
Solvent Atoms | 57 |
Heterogen Atoms | 236 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
MOLREP | phasing |
CNS | refinement |
MOSFLM | data reduction |
SCALA | data scaling |