Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 2BJ1 | PDB ENTRY 2BJ1 |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | | 7.5 | | pH 7.50 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.26 | 45.49 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 75.783 | α = 90 |
| b = 54.322 | β = 116.06 |
| c = 77.276 | 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 | RIGAKU RAXIS-V | | 2004-04-10 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B1 | | SPring-8 | BL26B1 |
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 | 2.2 | 30 | 97.8 | 0.05 | 21.9 | 3.1 | | 28283 | | -1 | 15.2 |
| 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 | 2.2 | 2.28 | 94.7 | | 0.28 | 4.5 | 2.5 | |
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-Free (Depositor) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2BJ1 | 2.2 | 29.25 | 28011 | 1415 | 96.8 | 0.218 | 0.218 | 0.268 | RANDOM | 54.1 |
| 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] |
|---|
| -3.62 | | 11.31 | 4.82 | | -1.2 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| c_dihedral_angle_d | 21.7 |
| c_scangle_it | 8.68 |
| c_scbond_it | 6.25 |
| c_mcangle_it | 5.7 |
| c_mcbond_it | 3.96 |
| c_angle_deg | 1.2 |
| c_improper_angle_d | 0.63 |
| c_bond_d | 0.007 |
| c_bond_d_na | |
| c_bond_d_prot | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| c_dihedral_angle_d | 21.7 |
| c_scangle_it | 8.68 |
| c_scbond_it | 6.25 |
| c_mcangle_it | 5.7 |
| c_mcbond_it | 3.96 |
| c_angle_deg | 1.2 |
| c_improper_angle_d | 0.63 |
| c_bond_d | 0.007 |
| c_bond_d_na | |
| c_bond_d_prot | |
| c_angle_d | |
| c_angle_d_na | |
| c_angle_d_prot | |
| c_angle_deg_na | |
| c_angle_deg_prot | |
| c_dihedral_angle_d_na | |
| c_dihedral_angle_d_prot | |
| c_improper_angle_d_na | |
| c_improper_angle_d_prot | |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 4342 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 103 |
| Heterogen Atoms | 4 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| DM | phasing |
| CNS | phasing |
| CNS | refinement |
