1JGJ
CRYSTAL STRUCTURE OF SENSORY RHODOPSIN II AT 2.4 ANGSTROMS: INSIGHTS INTO COLOR TUNING AND TRANSDUCER INTERACTION
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1C3W |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | cubic lipid phase | 5.3 | 295 | CUBIC LIPID PHASE WITH MO, PRECIPITANT KCL, pH 5.3, cubic lipid phase, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.13 | 60.75 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 87.34 | ¦Á = 90 |
b = 130.81 | ¦Â = 90 |
c = 50.87 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARRESEARCH | ID13 | 2001-04-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID13 | ESRF | ID13 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.4 | 20 | 92.2 | 0.085 | 5.7 | 7.5 | 10704 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
2.4 | 2.44 | 92 | 0.44 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1C3W | 2.4 | 20 | 10704 | 901 | 92.2 | 0.233 | 0.233 | 0.28 | RANDOM |
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] | |
-4.69 | -3.962 | 8.651 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_scangle_it | 2.498 |
c_scbond_it | 2.078 |
c_mcangle_it | 1.735 |
c_angle_deg | 1.297 |
c_mcbond_it | 1.253 |
c_bond_d | 0.00835 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1638 |
Nucleic Acid Atoms | |
Solvent Atoms | 11 |
Heterogen Atoms | 34 |
Software
Software | |
---|---|
Software Name | Purpose |
X-PLOR | model building |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | phasing |