Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1AYF | PDB ENTRY 1AYF |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | | 6.5 | | pH 6.5 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.5 | 51 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 59.443 | α = 90 |
| b = 77.025 | β = 94.83 |
| c = 59.681 | 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 | 120 | IMAGE PLATE | RIGAKU | MIRRORS | 1996-04-01 | 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) | 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 | 40 | 92 | 0.076 | 27 | 3.8 | | 17191 | | | 44.2 |
| 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) |
|---|
| 2.5 | 2.59 | 57.4 | | 0.29 | 3.9 | 3.1 | |
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-Work (Depositor) | R-Free (Depositor) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1AYF | 2.5 | 40 | 2 | 15878 | 1646 | 84.9 | 0.233 | 0.298 | RANDOM | 44.5 |
| 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] |
|---|
| 16.64 | | -3.78 | -12.42 | | -3.22 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| c_dihedral_angle_d | 23.1 |
| c_scangle_it | 5.26 |
| c_mcangle_it | 4.2 |
| c_scbond_it | 4.15 |
| c_mcbond_it | 2.52 |
| c_angle_deg | 0.996 |
| c_improper_angle_d | 0.54 |
| c_bond_d | 0.004 |
| c_bond_d_na | |
| c_bond_d_prot | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| c_dihedral_angle_d | 23.1 |
| c_scangle_it | 5.26 |
| c_mcangle_it | 4.2 |
| c_scbond_it | 4.15 |
| c_mcbond_it | 2.52 |
| c_angle_deg | 0.996 |
| c_improper_angle_d | 0.54 |
| c_bond_d | 0.004 |
| 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 | 3266 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 132 |
| Heterogen Atoms | 16 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| AMoRE | phasing |
| CNS | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
