2F95
M intermediate structure of sensory rhodopsin II/transducer complex in combination with the ground state structure
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1H2S | PDB Entry: 1H2S |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.8 | 296 | 150 MM NACL, 25 MM NAKPI 5.1 0.8% B-OCTYLGLUCOSID , MONOVACCENIN (CUBIC PHASE) PRECIPITATED BY 1 M NA/KPI 5.8 ,in cubic lipidic phase, temperature 296K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.8 | 31.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 124.62 | α = 90 |
b = 46.9 | β = 90 |
c = 53.85 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | ADSC QUANTUM 4 | 2004-09-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.934 | ESRF | ID14-1 |
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 | 2.2 | 22.01 | 97.9 | 0.085 | 3.9 | 16493 | 16147 | 2 | 1.8 | 25.2 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.2 | 2.26 | 99.4 | 0.414 | 3.9 |
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 (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB Entry: 1H2S | 2.2 | 22.01 | 2 | 16147 | 15688 | 767 | 94 | 0.219 | 0.217 | 0.217 | 0.241 | RANDOM | 27.9 |
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] | |
4.38 | -0.25 | -4.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 16.5 |
c_scangle_it | 2.3 |
c_mcangle_it | 1.81 |
c_scbond_it | 1.73 |
c_mcbond_it | 1.16 |
c_angle_deg | 1.1 |
c_improper_angle_d | 0.84 |
c_bond_d | 0.007 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2020 |
Nucleic Acid Atoms | |
Solvent Atoms | 33 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |
CNS | phasing |