Crystal structure of L.donovani Hypoxanthine-guanine phosphoribosyl transferase (HGPRT)
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details | 
| experimental model | PDB | 1PZM | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details | 
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 288 | 0.1M Sodium cacodylate, 0.2 M Ammonium sulfate, 20% PEG 4000 | 
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content | 
| 3.64 | 70.39 | 
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) | 
| a = 80.8 | α = 90 | 
| b = 80.8 | β = 90 | 
| c = 344.321 | γ = 120 | 
| Symmetry | |
|---|---|
| Space Group | P 65 2 2 | 
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | Monochromator | 2019-02-13 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline | 
| 1 | SYNCHROTRON | ELETTRA BEAMLINE 11.2C | 0.9784 | ELETTRA | 11.2C | 
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 | 2.76 | 44.373 | 93.7 | 0.04166 | 10.15 | 1.9 | 17049 | 52.65 | |||||||||||
| 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 | 2.76 | 2.86 | 98.1 | 0.2919 | 1.8 | ||||||||||||||
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-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1PZM | 2.76 | 44.37 | 1.34 | 17043 | 864 | 93.8 | 0.183 | 0.181 | 0.18 | 0.225 | 0.23 | |||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation | 
| f_dihedral_angle_d | 10.59 | 
| f_angle_d | 0.933 | 
| f_chiral_restr | 0.054 | 
| f_bond_d | 0.008 | 
| f_plane_restr | 0.005 | 
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number | 
| Protein Atoms | 2729 | 
| Nucleic Acid Atoms | |
| Solvent Atoms | 109 | 
| Heterogen Atoms | 43 | 
Software
| Software | |
|---|---|
| Software Name | Purpose | 
| PHENIX | refinement | 
| iMOSFLM | data reduction | 
| Aimless | data scaling | 
| PHASER | phasing | 














