X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1AMY | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 6.7 | pH 6.7 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.67 | 75 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 135.2 | α = 90 |
| b = 135.2 | β = 90 |
| c = 79.6 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 31 2 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 288 | AREA DETECTOR | SIEMENS | 1992-04-20 | M | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RUH2R | |||
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 | 2.729 | 90.5 | 0.092 | 0.092 | 16.6 | 2.9 | 17688 | 1 | |||||||||||
| 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) | ||||||||||
| 2.729 | 2.9 | 44.8 | 0.27 | 0.27 | 1.7 | 1.5 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | REFINEMENT DIFFERENCE FOURIER | THE VERSION OF X-PLOR (2.1) ORIGINALLY USED FOR REFINEMENT THE FREE R TEST WAS NOT AN OPTION. THEREFORE WE HAVE GIVEN THE OVERALL R FACTOR (TEST+WORKING) INSTEAD OF (WORK) TOGETHER WITH AN ESTIMATE OF THE FREE R (TEST) VALUE BASED ON A SIMULATED ANNEALING REFINEMENT WITH A NEWER VERSION OF X-PLOR (3.1). | 1AMY | 2.8 | 10 | 1 | 17688 | 1729 | 86.4 | 0.151 | 0.151 | 0.14 | 0.249 | 0.14 | RANDOM | 20.1 | |||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| x_dihedral_angle_d | 23.6 |
| x_angle_deg | 3.2 |
| x_bond_d | 1.5 |
| x_improper_angle_d | 1.4 |
| 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 | 3184 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 148 |
| Heterogen Atoms | 58 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| X-PLOR | model building |
| X-PLOR | refinement |
| XENGEN | data reduction |
| NIELSEN | data reduction |
| XUONG) | data reduction |
| XENGEN | data scaling |
| X-PLOR | phasing |
