2I36
Crystal structure of trigonal crystal form of ground-state rhodopsin
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 6.3 | 278 | 80 mM MES, pH 6.3, 110 mM N-nonyl-beta-D-glucoside, 200 mM zinc acetate, 0.1% sodium azide, 16 mM beta-mercaptoethanol, 2.6% Merpol HCS, equilibrated against 3.1-3.3 M ammonium sulfate, VAPOR DIFFUSION, temperature 278K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.5 | 72.5 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 159.866 | α = 90 |
| b = 159.866 | β = 90 |
| c = 142.15 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 31 1 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 77 | CCD | ADSC QUANTUM 315 | 2004-04-04 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.97970 | SSRL | BL11-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 4 | 50 | 99.7 | 0.087 | 21.1 | 10.6 | 17705 | 17705 | 185 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1 | 4 | 4.15 | 100 | ||||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1HZX | 4.1 | 30 | 16375 | 16375 | 832 | 99.82 | 0.38367 | 0.38367 | 0.38229 | 0.41153 | RANDOM | 185 | ||||
| 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] | |
| -13.16 | -6.58 | -13.16 | 19.74 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 40.202 |
| r_dihedral_angle_3_deg | 21.531 |
| r_dihedral_angle_4_deg | 17.059 |
| r_dihedral_angle_1_deg | 6.376 |
| r_angle_refined_deg | 1.327 |
| r_symmetry_vdw_refined | 0.342 |
| r_nbtor_refined | 0.316 |
| r_nbd_refined | 0.23 |
| r_symmetry_hbond_refined | 0.17 |
| r_xyhbond_nbd_refined | 0.169 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 7665 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 218 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| SSRL | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
