1QM8
Structure of Bacteriorhodopsin at 100 K
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1BM1 | PDB ENTRY 1BM1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 5.2 | THE CRYSTALLIZATION CONSISTS OF TWO STEPS. FIRST, A MIXTURE OF 5 MG/ML PURPLE MEMBRANE, 0.25% OTG, 1 M AMMONIUM SULFATE, 0.16 M NACL, 0.04 M SODIUM CITRATE (PH5.2) , 0.04% NAN3 WAS INCUBATED AND 15% TREHALOSE AT 305K FOR 5 DAYS. THIS RESULTED IN THE FORMATION OF SPHERICAL VESICLES WITH A DIAMETER OF 50 NM. AFTER SEDIMENTAL MATERIALS WERE REMOVED BY CENTRIFUGATION (4000G X 10 MIN), A SUSPENSION OF THE SPHERICAL VESICLES WAS COOLED TO 278K AND CONCENTRATED BY VAPOR DIFFUSION AGAINST A RESERVOIR SOLUTION CONTAINING 2.0 M AMMONIUM SULFATE 0.08M SODIUM CITRATE (PH 5.2) AND 30% TREHALOSE. INCUBATION FOR A COUPLE OF MONTHS YIELDED HEXAGONAL CRYSTALS. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.15 | 60.96 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 102.1 | ¦Á = 90 |
b = 102.1 | ¦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 | IMAGE PLATE | FUJI FILM | MIRRORS | 1998-05-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44B2 | SPring-8 | BL44B2 |
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 | 2.5 | 46.6 | 100 | 0.057 | 9.9 | 12500 | 49.2 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.5 | 2.65 | 99.9 | 0.387 | 9.9 |
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 1BM1 | 2.5 | 8 | 11888 | 610 | 100 | 0.251 | 0.251 | 0.278 | RANDOM |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-28.5 | -14.2 | -28.5 | 4.9 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 20.636 |
x_angle_deg | 1.419 |
x_improper_angle_d | 1.206 |
x_bond_d | 0.01 |
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 | 1759 |
Nucleic Acid Atoms | |
Solvent Atoms | 23 |
Heterogen Atoms | 257 |
Software
Software | |
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Software Name | Purpose |
X-PLOR | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
X-PLOR | phasing |