4RZG
Crystal Structure Analysis of the DNPA-bounded NUR77 Ligand binding Domain
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 4.2 | 277 | PEG4000, Sodium citrate, Glycerol, pH 4.2, vapor diffusion, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.19 | 61.48 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 74.228 | α = 90 |
| b = 76.529 | β = 90 |
| c = 128.677 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
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 | MARMOSAIC 325 mm CCD | 2013-03-19 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRF BEAMLINE BL17U | 1.5418 | SSRF | BL17U |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.7 | 50 | 97.08 | 19695 | 19120 | -3 | -3 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.7 | 49.3 | 19695 | 19120 | 1040 | 97.08 | 0.2146 | 0.2146 | 0.2117 | 0.2696 | RANDOM | 47.88 | |||||
| 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] | |
| 0.51 | 0.22 | -0.73 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 38.531 |
| r_dihedral_angle_3_deg | 19.81 |
| r_dihedral_angle_4_deg | 17.917 |
| r_mcangle_it | 5.734 |
| r_dihedral_angle_1_deg | 5.481 |
| r_mcbond_it | 3.68 |
| r_mcbond_other | 3.67 |
| r_angle_refined_deg | 1.698 |
| r_angle_other_deg | 1.133 |
| r_chiral_restr | 0.075 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3635 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 141 |
| Heterogen Atoms | 45 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SCALA | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASES | phasing |
