3A7K
Crystal structure of halorhodopsin from Natronomonas pharaonis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1E12 | PDB ENTRY 1e12 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 293 | A DROP CONTAINING 1MG/ML PROTEIN, 1M AMMONIUM SULFATE, 0.16M NACL, 0.04M TRIS-HCL, 0.04% NAN2, 5MG/ML NONYL GLUCOSIDE WAS CONCENTRATED BY VAPOR DIFFUSION AGAINST A RESERVE SOLUTION CONTAINING 2.6 M AMMONIUM SULFATE, 0.16M NACL, 0.04M TRIS-HCL, PH 8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.2 | 61.59 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 151.83 | ¦Á = 90 |
b = 99.77 | ¦Â = 127.67 |
c = 99.27 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | mirrors | 2009-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.0 | SPring-8 | BL41XU |
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 | 60.1 | 99.5 | 0.072 | 0.072 | 9.9 | 2.7 | 79092 | 31.2 |
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 | 2.11 | 100 | 0.556 | 0.556 | 2 | 2.7 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1e12 | 2 | 15 | 78925 | 78528 | 3975 | 99.6 | 0.249 | 0.274 | RANDOM | 49.222 |
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] | |
2.094 | -12.748 | 2.659 | -4.754 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 2.394 |
c_mcangle_it | 1.895 |
c_scbond_it | 1.717 |
c_mcbond_it | 1.28 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5868 |
Nucleic Acid Atoms | |
Solvent Atoms | 144 |
Heterogen Atoms | 666 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
CNS | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
CNS | phasing |