Human Adenine Phosphoribosyltransferase Complexed with AMP, in Space Group P1 at 1.76 A Resolution
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 291 | 15.0 % (V/V) glycerol, 25.5 % (w/V) polyethylene glycol 4000, 0.17 mol/L sodium acetate and 0.085 mol/L Tris-HCl pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 291 K, pH 8.50 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.17 | 42.91 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 47.06 | α = 75.41 |
| b = 47.47 | β = 68.42 |
| c = 47.84 | γ = 61.49 |
| Symmetry | |
|---|---|
| Space Group | P 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | IMAGE PLATE | MARRESEARCH | M | SINGLE WAVELENGTH | ||||||||
| 2 | 1 | |||||||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU | 1.5418 | ||
| 2 | SYNCHROTRON | LNLS BEAMLINE D03B-MX1 | 1.4538 | LNLS | D03B-MX1 |
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 | 1.76 | 44 | 31837 | ||||||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.76 | 44 | 30208 | 1629 | 95.5 | 0.16 | 0.157 | 0.17 | 0.211 | RANDOM | 17.51 | ||||||
| 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] | |
| -0.48 | 0.96 | -0.34 | -0.37 | -0.24 | 0.31 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.747 |
| r_dihedral_angle_4_deg | 22.271 |
| r_dihedral_angle_3_deg | 15.397 |
| r_dihedral_angle_1_deg | 6.317 |
| r_scangle_it | 4.006 |
| r_scbond_it | 2.758 |
| r_angle_refined_deg | 1.932 |
| r_mcangle_it | 1.607 |
| r_mcbond_it | 1.467 |
| r_angle_other_deg | 0.962 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2717 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 355 |
| Heterogen Atoms | 47 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
