6I9Y
The 2.14 A X-ray crystal structure of Sporosarcina pasteurii urease in complex with Au(I) ions
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 5G4H |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.3 | 293 | The protein-ligand complex in 50 mM HEPES buffer, pH 7.50 (also containing 5% (v/v) DMSO), was diluted with an equal volume of 1.5 M ammonium sulfate containing the same concentration of ligand and DMSO. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.81 | 56.24 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 132.291 | α = 90 |
b = 132.291 | β = 90 |
c = 190.435 | 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 EIGER X 4M | 2018-06-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 0.9677 | ESRF | ID30B |
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 | 2.14 | 45.8 | 100 | 0.139 | 0.157 | 0.07 | 0.997 | 11.2 | 8.9 | 54809 | 32.3 |
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 | 2.14 | 2.2 | 100 | 1.509 | 1.71 | 0.785 | 0.627 | 1.5 | 8.8 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 5G4H | 2.14 | 45.8 | 51984 | 2768 | 99.92 | 0.17262 | 0.17074 | 0.20801 | RANDOM | 40.28 |
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] | |
0.91 | 0.46 | 0.91 | -2.96 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.574 |
r_dihedral_angle_4_deg | 14.901 |
r_dihedral_angle_3_deg | 13.202 |
r_dihedral_angle_1_deg | 5.639 |
r_long_range_B_refined | 5.428 |
r_mcangle_it | 1.919 |
r_scbond_it | 1.857 |
r_mcbond_it | 1.202 |
r_angle_refined_deg | 1.091 |
r_chiral_restr | 0.076 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6047 |
Nucleic Acid Atoms | |
Solvent Atoms | 335 |
Heterogen Atoms | 85 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
REFMAC | phasing |