4PFQ
Crystal structure of hypoxanthine phosphoribosyltransferase from Brachybacterium faecium DSM 4810, NYSGRC Target 029763.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 298 | 0.2 M Mg-chloride, 20% PEG 3350 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.11 | 41.67 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 51.21 | α = 90 |
| b = 123.587 | β = 90.45 |
| c = 123.285 | 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 | RAYONIX MX225HE | 2013-08-09 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.9791 | APS | 31-ID |
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 | 2.1 | 50 | 95.9 | 0.117 | 12.6 | 4.7 | 86164 | ||||||||||||
| 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 | 2.1 | 2.14 | 92.1 | 0.644 | 4.4 | 4154 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.1 | 33.31 | 86139 | 4349 | 93.8 | 0.176 | 0.173 | 0.213 | RANDOM | 44.11 | |||||||
| 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] | |
| -8.39 | -1.06 | 4.02 | 4.37 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.381 |
| r_dihedral_angle_4_deg | 20.272 |
| r_dihedral_angle_3_deg | 12.37 |
| r_dihedral_angle_1_deg | 6.603 |
| r_mcangle_it | 5.112 |
| r_mcbond_it | 3.91 |
| r_mcbond_other | 3.91 |
| r_angle_refined_deg | 1.887 |
| r_angle_other_deg | 1.872 |
| r_chiral_restr | 0.107 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 11272 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 543 |
| Heterogen Atoms | 12 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| SCALEPACK | data scaling |
| PDB_EXTRACT | data extraction |
| PHENIX | model building |
| SHELX | phasing |
| SHELXD | phasing |
