2C1Y
Structure of PDI-related Chaperone, Wind mutant-Y55K
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1OVN | PDB ENTRY 1OVN |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 8.2 | 0.1M TRIS-HCL PH 8.2-8.8 25 MM MGCL2 10% PEG4000 5% GLYCEROL | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.51 | 64.72 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 35.421 | α = 90 |
| b = 119.095 | β = 100.53 |
| c = 64.034 | 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 | CCD | MARRESEARCH | 2005-01-18 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | EMBL/DESY, HAMBURG | X13 | |
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 | 2.25 | 20 | 97.8 | 0.06 | 16.83 | 4.67 | 22938 | 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 | 2.25 | 2.34 | 91.3 | 0.27 | 3.51 | 2.62 | |||||||||||||
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 1OVN | 2.25 | 20 | 22938 | 1220 | 99.9 | 0.226 | 0.223 | 0.23 | 0.292 | 0.29 | THIN SHELLS | 45.38 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| 0.7 | 2.28 | -1.09 | 1.22 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.944 |
| r_dihedral_angle_3_deg | 20.948 |
| r_dihedral_angle_4_deg | 19.681 |
| r_dihedral_angle_1_deg | 9.15 |
| r_scangle_it | 8.949 |
| r_scbond_it | 6.449 |
| r_mcangle_it | 4.068 |
| r_angle_refined_deg | 2.73 |
| r_mcbond_it | 2.598 |
| r_nbtor_refined | 0.317 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2649 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 55 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
