7B59
X-ray crystal structure of Sporosarcina pasteurii urease inhibited by Ag(PEt3)Br determined at 1.63 Angstroms
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6G48 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | THE PROTEIN-LIGAND (600 microM) COMPLEX IN 50 mM HEPES BUFFER, PH 7.50 (ALSO CONTAINING 1% (V/V) DMSO), DILUTED 1:1 WITH A SOLUTION OF 1.4 M AMMONIUM SULFATE ALSO CONTAINING THE SAME CONCENTRATION OF LIGAND AND DMSO. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.76 | 55.41 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 131.41 | α = 90 |
b = 131.41 | β = 90 |
c = 189.416 | 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 | PIXEL | DECTRIS PILATUS 6M | 2019-11-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.9762 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.63 | 113.8 | 100 | 0.131 | 0.138 | 0.043 | 1 | 19.2 | 19.6 | 119894 | 23.1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.63 | 1.66 | 99.8 | 4.326 | 4.572 | 1.47 | 0.702 | 1 | 18.4 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6G48 | 1.63 | 113.8 | 119803 | 5954 | 99.882 | 0.15 | 0.1487 | 0.1774 | 28.432 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
1.07 | 0.535 | 1.07 | -3.47 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.534 |
r_dihedral_angle_4_deg | 18.521 |
r_dihedral_angle_3_deg | 13.384 |
r_dihedral_angle_1_deg | 7.264 |
r_lrange_it | 5.872 |
r_lrange_other | 5.695 |
r_scangle_it | 4.934 |
r_scangle_other | 4.544 |
r_scbond_it | 3.573 |
r_scbond_other | 3.272 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6047 |
Nucleic Acid Atoms | |
Solvent Atoms | 706 |
Heterogen Atoms | 151 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
REFMAC | phasing |