1XJQ
ADP Complex OF HUMAN PAPS SYNTHETASE 1
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1X6V | PDB ENTRY 1X6V |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 5.6 | 290 | 1 mM ADP was soaked into native crystals (PDB ENTRY 1X6V) for one hour, pH 5.60, VAPOR DIFFUSION, HANGING DROP, temperature 290K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.9 | 57 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 78.5 | ¦Á = 90 |
| b = 82.5 | ¦Â = 105 |
| c = 133 | ¦Ã = 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 | ADSC QUANTUM 4 | 2003-03-01 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.05 | 20 | 97.5 | 0.104 | 0.083 | 13.6 | 7.4 | 100470 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 2.05 | 2.1 | 89.5 | 0.609 | 0.741 | 2.48 | 5.8 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | MOLECULAR REPLACEMENT WITH INITIAL MERCURY PHASES | THROUGHOUT | PDB ENTRY 1X6V | 2.06 | 129.1 | 100470 | 92501 | 4869 | 96.56 | 0.17383 | 0.17135 | 0.22147 | RANDOM | 37.726 | |||||
| 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] | |
| 1.6 | 1.22 | 0.77 | -1.74 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_1_deg | 7.54 |
| r_scangle_it | 3.694 |
| r_mcangle_it | 3.549 |
| r_angle_refined_deg | 2.474 |
| r_scbond_it | 2.411 |
| r_mcbond_it | 2.303 |
| r_angle_other_deg | 1.319 |
| r_symmetry_hbond_refined | 0.287 |
| r_nbd_other | 0.283 |
| r_symmetry_vdw_other | 0.249 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 9206 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 684 |
| Heterogen Atoms | 81 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| X-GEN | data scaling |
| XDS | data reduction |
| XFIT | data reduction |
| REFMAC | refinement |
| X-GEN | data reduction |
| XDS | data scaling |
