X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1PKY | PDB ENTRY 1PKY |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 4.8 | 6% PEG 4000, 20MM AMMONIUM SULPHATE, 15% GLYCEROL, 20MM SODIUM ACETATE PH 4.8 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.33 | 62.8 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 121.649 | α = 90 |
| b = 132.638 | β = 97.11 |
| c = 180.996 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
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 | MARRESEARCH | BENT FUSED QUARTZ SINGLE SEGMENT MIRROR | 1997-12-15 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SRS BEAMLINE PX7.2 | SRS | PX7.2 | |
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 | 2.35 | 30 | 68 | 0.089 | 5.4 | 1.5 | 160789 | ||||||||||||
| 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) | |||||||||||
| 1 | 2.35 | 2.48 | 47.4 | 0.308 | 2.4 | 1.2 | |||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | OTHER | THROUGHOUT | PDB ENTRY 1PKY | 2.35 | 30 | 160789 | 8074 | 67.9 | 0.209 | 0.209 | 0.22 | 0.256 | RANDOM | 48.9 | |||||
| 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] | |
| -12.518 | -4.1509 | 11.1994 | 1.3186 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| x_dihedral_angle_d | 24 |
| x_angle_deg | 1.4 |
| x_improper_angle_d | 1.2 |
| x_bond_d | 0.009 |
| x_bond_d_na | |
| x_bond_d_prot | |
| x_angle_d | |
| x_angle_d_na | |
| x_angle_d_prot | |
| x_angle_deg_na | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 29994 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 2952 |
| Heterogen Atoms | 40 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| AMoRE | phasing |
| FFT | model building |
| SHELXS | phasing |
| MLPHARE | phasing |
| DM | model building |
| X-PLOR | refinement |
| DENZO | data reduction |
| CCP4 | data scaling |
| FFT | phasing |
| DM | phasing |
