Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1UBQ | PDB ENTRY 1UBQ |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | | 4.8 | | pH 4.8 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.1 | 41 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 45.804 | α = 90 |
| b = 64.972 | β = 96.66 |
| c = 48.573 | 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 | MACSCIENCE | MIRRORS | | 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 | 1.6 | 20 | 97.8 | 0.067 | 0.067 | 20 | 6.9 | | 36579 | | -2 | 21.1 |
| 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) |
|---|
| 1 | 1.6 | 1.63 | 93.7 | | 0.452 | 0.452 | 1.9 | 6.9 | |
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 (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1UBQ | 1.6 | 100 | 36560 | 1109 | 97.8 | 0.219 | 0.219 | 0.2189 | 0.3 | 0.2904 | RANDOM | 23.2 |
| 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 | 25.3 |
| x_angle_deg | 1.3 |
| x_improper_angle_d | 1.15 |
| x_bond_d | 0.006 |
| x_bond_d_na | |
| x_bond_d_prot | |
| x_angle_d | |
| x_angle_d_na | |
| x_angle_d_prot | |
| x_angle_deg_na | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| x_dihedral_angle_d | 25.3 |
| x_angle_deg | 1.3 |
| x_improper_angle_d | 1.15 |
| x_bond_d | 0.006 |
| 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 | |
| x_mcbond_it | |
| x_mcangle_it | |
| x_scbond_it | |
| x_scangle_it | |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2349 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 193 |
| Heterogen Atoms | 22 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| AMoRE | phasing |
| X-PLOR | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
