1QKP
HIGH RESOLUTION X-RAY STRUCTURE OF AN EARLY INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | LIPIDIC CUBIC PHASE | 5.6 | 293 | PROTEIN FROM THE PURPLE MEMBRANE WAS DELIPIDATED AND SOLUBILIZED IN OCTYL GLUCOSIDE. PROTEIN WAS CRYSTALLIZED FROM 60 - 70% (W/W) MONOOLEIN, 0.7 - 4.0 M NA/K - PHOSPHATE IN A PHOSPHATE BUFFER AT PH 5.6, AT 20C AND IN THE DARK. THE MIXTURE WAS CENTRIFUGED AT 10000G FOR 150 MN PRIOR TO CRYSTALLISATION. |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.39 | 48 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 61.06 | α = 90 |
| b = 61.06 | β = 90 |
| c = 110.57 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 63 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 110 | CCD | MARRESEARCH | 1999-02-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-3 | ESRF | ID14-3 | |
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 | 2.1 | 38 | 99.8 | 0.055 | 10.1 | 4.9 | 13653 | 35 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.1 | 2.2 | 99.6 | 0.37 | 2.1 | 4.9 | |||||||||||||
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 | 1QHJ | 2.1 | 38 | 13628 | 642 | 99.7 | 0.2222 | 0.2222 | 0.255 | THE SAME TEST SET AS FOR THE REFINEMENT OF 1QHJ WAS USED | 36.5 | ||||||
| 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] | |
| 4.566 | 0.292 | 4.566 | -9.132 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_dihedral_angle_d | 18.2305 |
| c_scangle_it | 2.023 |
| c_scbond_it | 1.769 |
| c_mcangle_it | 1.422 |
| c_angle_deg | 1.1637 |
| c_mcbond_it | 1.081 |
| c_improper_angle_d | 0.7917 |
| c_bond_d | 0.0091 |
| c_bond_d_na | |
| c_bond_d_prot | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1751 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 27 |
| Heterogen Atoms | 20 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CNS | refinement |
| DENZO | data reduction |
| CCP4 | data scaling |
| CNS | phasing |
