X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4XEM | PDB entry 4XEM |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 8 | 310 | 25% PEG6000, 100 mM Tris-HCl, pH 8.0 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.04 | 39.74 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 108.33 | α = 90 |
| b = 67.27 | β = 136.23 |
| c = 86.35 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 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 | MAR scanner 345 mm plate | 2011-12-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.03 | 59.734 | 99.2 | 0.06 | 0.069 | 0.034 | 15.7 | 3.9 | 27565 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 2.03 | 2.14 | 94.8 | 0.32 | 0.32 | 0.373 | 0.189 | 2.4 | 3.7 | 3800 | |||||||||
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 4XEM | 2.03 | 59.73 | 26163 | 1390 | 99.44 | 0.1817 | 0.1799 | 0.19 | 0.2146 | 0.22 | RANDOM | 26.974 | ||||
| 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] | |
| -0.75 | -1.12 | 0.62 | -1.5 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.807 |
| r_dihedral_angle_4_deg | 17.112 |
| r_dihedral_angle_3_deg | 12.345 |
| r_dihedral_angle_1_deg | 4.716 |
| r_angle_refined_deg | 1.227 |
| r_chiral_restr | 0.072 |
| r_bond_refined_d | 0.007 |
| r_gen_planes_refined | 0.004 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2996 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 245 |
| Heterogen Atoms | 29 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SCALA | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| iMOSFLM | data reduction |
| MOLREP | phasing |
