1AP9
X-RAY STRUCTURE OF BACTERIORHODOPSIN FROM MICROCRYSTALS GROWN IN LIPIDIC CUBIC PHASES
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BRD | PDB ENTRY 2BRD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.6 | PROTEIN FROM THE PURPLE MEMBRANE WAS DELIPIDATED AND SOLUBILIZED IN OCTYL GLUCOSIDE. PROTEIN WAS CRYSTALLIZED FROM 60 - 70% (W/W) MONOOLEIN, 0.7 - 4.0 M NA/K - PHOSPHATE IN A PHOSPHATE BUFFER AT PH 5.6, AT 20C AND IN THE DARK. THE MIXTURE WAS CENTRIFUGED AT 10000G FOR 150 MN PRIOR TO CRYSTALLISATION. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.76 | α = 90 |
b = 61.76 | β = 90 |
c = 104.16 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | ELLIPSOIDAL MIRROR | 1996-08-16 | M |
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 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 | 2.35 | 10 | 91.2 | 0.1 | 4.7 | 2 | 8045 | 45.5 |
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 | 2.35 | 2.56 | 90.4 | 0.266 | 2.4 | 1.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 2BRD | 2.35 | 5 | 2.5 | 6564 | 300 | 77.8 | 0.2582 | 0.2582 | 0.317 | RANDOM | 75 |
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 |
x_dihedral_angle_d | 20.82 |
x_angle_deg | 1.491 |
x_improper_angle_d | 1.188 |
x_bond_d | 0.008 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1694 |
Nucleic Acid Atoms | |
Solvent Atoms | 26 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
X-PLOR | model building |
X-PLOR | refinement |
DENZO | data reduction |
CCP4 | data scaling |
X-PLOR | phasing |