1GZM
Structure of Bovine Rhodopsin in a Trigonal Crystal Form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1F88 | PDB ENTRY 1F88 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | VAPOUR DIFFUSION IN SITTING DROPS OF 15 MG/ML PROTEIN AND 0.2% C8E4, 0.05%LDAO AGAINST 0.8M LI2SO4, 1.6% PEG8000 AND 20% GLYCEROL, pH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.07 | 49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 103.82 | α = 90 |
b = 103.82 | β = 90 |
c = 76.59 | γ = 120 |
Symmetry | |
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Space Group | P 31 |
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 | MARRESEARCH | 2000-10-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID13 | ESRF | ID13 |
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 | 2.65 | 46 | 97 | 0.119 | 11 | 4.4 | 26026 | 58.2 |
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 | 2.65 | 2.79 | 86 | 0.434 | 1.4 | 1.6 |
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 1F88 | 2.65 | 46 | 24704 | 1322 | 97 | 0.2015 | 0.2015 | 0.2353 | RANDOM | 56 |
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] | |
-4.454 | -8.526 | -4.454 | 8.907 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 19 |
c_scangle_it | 3.81 |
c_mcangle_it | 3.13 |
c_scbond_it | 2.39 |
c_mcbond_it | 1.78 |
c_angle_deg | 1.3 |
c_improper_angle_d | 0.88 |
c_bond_d | 0.008 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5212 |
Nucleic Acid Atoms | |
Solvent Atoms | 40 |
Heterogen Atoms | 540 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
AMoRE | phasing |