4AC7
The crystal structure of Sporosarcina pasteurii urease in complex with citrate
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 6.3 | 1.8 M AMMONIUM SULPHATE, 100 MM CITRATE PH 6.3, 50 MM NA2SO3 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.76 | 55.46 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 131.555 | α = 90 |
| b = 131.555 | β = 90 |
| c = 189.521 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 63 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 | CCD | MARRESEARCH | 2011-09-30 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | PETRA III, EMBL c/o DESY | P14 (MX2) | |
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 | 1.5 | 113.93 | 99.9 | 0.1 | 22.6 | 15.5 | 153738 | 2 | |||||||||||
| 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 | 1.5 | 1.58 | 100 | 0.58 | 4 | 9.9 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 1S3T DEPLETED OF WATERS SULPHATES AND BORATE WAS USED AS A MODEL FOR RIGID BODY REFINEMENT FOLLOWED BY REFINEMENT AND MODEL BUILDING | 1.5 | 113.93 | 145792 | 7712 | 99.86 | 0.11847 | 0.11703 | 0.14605 | RANDOM | 13.109 | ||||||
| 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] | |
| 0.52 | 0.26 | 0.52 | -0.78 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.847 |
| r_sphericity_free | 24.641 |
| r_dihedral_angle_4_deg | 16.322 |
| r_dihedral_angle_3_deg | 11.53 |
| r_sphericity_bonded | 7.086 |
| r_dihedral_angle_1_deg | 6.259 |
| r_rigid_bond_restr | 2.383 |
| r_angle_refined_deg | 1.448 |
| r_angle_other_deg | 0.947 |
| r_chiral_restr | 0.087 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6014 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 671 |
| Heterogen Atoms | 76 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| REFMAC | phasing |
