3EWZ
human orotidyl-5'-monophosphate decarboxylase in complex with 5-cyano-UMP
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8 | 300 | 0.1 M Tris-HCl pH 8.0, 1.8 M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 300.0K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.58 | 52.34 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 71.557 | ¦Á = 90 |
| b = 60.793 | ¦Â = 99.29 |
| c = 136.087 | ¦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 | MARMOSAIC 225 mm CCD | 2008-05-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.0000 | SLS | X10SA |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.4 | 46.08 | 85.3 | 0.069 | 9.6 | 2.6 | 193472 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1.4 | 1.46 | 35.6 | 0.378 | 1.5 | 0.7 | 8026 | |||||||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.4 | 46.08 | 177695 | 9355 | 82.48 | 0.15593 | 0.1543 | 0.18701 | RANDOM | 10.678 | |||||||
| 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] | |
| -0.42 | -0.76 | -0.38 | 0.56 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.327 |
| r_dihedral_angle_4_deg | 15.341 |
| r_dihedral_angle_3_deg | 12.988 |
| r_dihedral_angle_1_deg | 5.992 |
| r_sphericity_free | 4.384 |
| r_scangle_it | 3.753 |
| r_angle_other_deg | 2.721 |
| r_scbond_it | 2.42 |
| r_sphericity_bonded | 1.851 |
| r_mcangle_it | 1.589 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8275 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1248 |
| Heterogen Atoms | 102 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| COMO | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| SADABS | data scaling |
