Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1LYA | PDB ENTRY 1LYA |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | | 7.5 | | pH 7.5 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 1.24 | 65 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 140.256 | α = 90 |
| b = 136.797 | β = 90 |
| c = 140.416 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 21 2 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 190 | IMAGE PLATE | MARRESEARCH | MIRRORS | 1997-07-09 | 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 | 2.5 | 20 | 73 | 0.108 | 0.108 | 6.95 | 3.2 | | 197513 | | 2 | |
| 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) |
|---|
| 2.5 | 2.59 | 41 | | 0.318 | 0.318 | 2 | 1.37 | |
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-Free (Depositor) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1LYA | 2.5 | 8 | 2 | 63094 | 6380 | 73 | 0.195 | 0.195 | 0.257 | RANDOM | |
| 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 | 26.2 |
| x_angle_deg | 1.9 |
| x_improper_angle_d | 1.3 |
| 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 | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| x_dihedral_angle_d | 26.2 |
| x_angle_deg | 1.9 |
| x_improper_angle_d | 1.3 |
| 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 | |
| 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 | 10328 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 557 |
| Heterogen Atoms | 60 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| X-PLOR | model building |
| X-PLOR | refinement |
| X-PLOR | phasing |
