X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1Q5U | PDB ENTRY 1Q5U |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 4.2 | 298 | 12% PEG1000, 0.1M lithium sulfate, 0.1M phosphate/citrate buffer, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 4.20 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.09 | 41.05 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 105.26 | α = 90 |
| b = 105.26 | β = 90 |
| c = 59.29 | 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 | 100 | IMAGE PLATE | RIGAKU RAXIS IV | MIRRORS | 2005-06-05 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RU200 | |||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 2.15 | 49.7 | 98.6 | 0.033 | 0.033 | 29.9 | 6.2 | 20238 | 1 | 27 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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) | ||||||||||
| 1 | 2.15 | 2.23 | 92.1 | 0.144 | 0.144 | 6 | 2.6 | ||||||||||||
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 (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1Q5U | 2.15 | 18.13 | 19126 | 19126 | 1034 | 98.4 | 0.212 | 0.21 | 0.23 | 0.257 | 0.27 | RANDOM | 30.84 | |||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| 0.03 | 0.01 | 0.03 | -0.04 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 27.801 |
| r_dihedral_angle_4_deg | 13.583 |
| r_dihedral_angle_3_deg | 11.892 |
| r_dihedral_angle_1_deg | 5.671 |
| r_scangle_it | 1.101 |
| r_angle_refined_deg | 0.902 |
| r_scbond_it | 0.697 |
| r_mcangle_it | 0.548 |
| r_mcbond_it | 0.31 |
| r_nbtor_refined | 0.309 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2643 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 236 |
| Heterogen Atoms | 29 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| d*TREK | data reduction |
| d*TREK | data scaling |
| MOLREP | phasing |
