Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1BK5 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | | 6 | | pH 6.0 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 3 | 59 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 78.549 | α = 90 |
| b = 89.675 | β = 90 |
| c = 100.562 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 21 21 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 288 | IMAGE PLATE | MARRESEARCH | | 1998-05-25 | 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) | 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 | 2.5 | 99 | 97 | 0.123 | 9.4 | 5.9 | | 144864 | | | 32 |
| 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) |
|---|
| 2.5 | 2.59 | 100 | | 0.631 | 1.7 | 2.8 | |
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 | 1BK5 | 2.5 | 40 | 24595 | 1686 | 97.6 | 0.189 | 0.189 | 0.24 | RANDOM | 40 |
| 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 | 22.3 |
| x_scangle_it | 6.88 |
| x_scbond_it | 4.77 |
| x_mcangle_it | 4.29 |
| x_mcbond_it | 2.81 |
| x_angle_deg | 1.1 |
| x_improper_angle_d | 0.64 |
| x_bond_d | 0.005 |
| x_bond_d_na | |
| x_bond_d_prot | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| x_dihedral_angle_d | 22.3 |
| x_scangle_it | 6.88 |
| x_scbond_it | 4.77 |
| x_mcangle_it | 4.29 |
| x_mcbond_it | 2.81 |
| x_angle_deg | 1.1 |
| x_improper_angle_d | 0.64 |
| x_bond_d | 0.005 |
| x_bond_d_na | |
| x_bond_d_prot | |
| x_angle_d | |
| x_angle_d_na | |
| x_angle_d_prot | |
| x_angle_deg_na | |
| x_angle_deg_prot | |
| x_dihedral_angle_d_na | |
| x_dihedral_angle_d_prot | |
| x_improper_angle_d_na | |
| x_improper_angle_d_prot | |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 3351 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 179 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| X-PLOR | model building |
| X-PLOR | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| X-PLOR | phasing |
