2ZZL
Structure of bacteriorhodopsin's M intermediate at pH 7
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1IW9 | PDB ENTRY 1iw9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | Membrane fusion method | 5.2 | 293 | 2.2M ammonium sulfate, 0.1M sodium citrate, 0.16M potasium chloride, 3M ammonium sulfate, 0.1M HEPES pH 7, liquid propane, Membrane fusion method, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3 | 59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.21 | α = 90 |
b = 102.21 | β = 90 |
c = 112.48 | γ = 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 | MAR CCD 165 mm | 2009-01-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 0.912 | Photon Factory | AR-NW12A |
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 | 2.03 | 44.2 | 93.7 | 0.084 | 0.084 | 22.8 | 14.4 | 23074 | 21621 | 31.68 |
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) | ||||||||||
2.03 | 2.43 | 71.4 | 0.521 | 0.521 | 4.5 | 14 | 2355 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1iw9 | 2.03 | 15 | 23984 | 18197 | 18197 | 88.3 | 0.207 | 0.207 | 0.238 | RANDOM | 41.47 |
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] | |
-4.469 | -5.345 | -4.469 | 8.937 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 17.5706 |
c_angle_deg | 1.17599 |
c_improper_angle_d | 0.76763 |
c_bond_d | 0.006981 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1765 |
Nucleic Acid Atoms | |
Solvent Atoms | 40 |
Heterogen Atoms | 322 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
CNS | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
CNS | phasing |