7P7O

X-RAY CRYSTAL STRUCTURE OF SPOROSARCINA PASTEURII UREASE INHIBITED BY THE GOLD(I)-DIPHOSPHINE COMPOUND Au(PEt3)2Cl DETERMINED AT 1.87 ANGSTROMS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OL4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293THE PROTEIN-LIGAND (1.2 mM) COMPLEX IN 50 MM HEPES BUFFER, PH 7.50 (ALSO CONTAINING 10% (V/V) DMSO), DILUTED 1:1 WITH A SOLUTION OF 1.2-1.7 M AMMONIUM SULFATE ALSO CONTAINING THE SAME CONCENTRATION OF LIGAND AND DMSO.
Crystal Properties
Matthews coefficientSolvent content
2.7655.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.797α = 90
b = 131.797β = 90
c = 189.381γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9762PETRA III, EMBL c/o DESYP13 (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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.871141000.1510.1590.0380.99917.917.48049826.89
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)RedundancyNumber Unique Reflections (All)
11.871.911003.0983.2960.7780.7441.517.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5ol41.8765.98580442400899.9640.1670.1650.210338.018
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]
1.3570.6791.357-4.404
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.067
r_dihedral_angle_4_deg18.889
r_rigid_bond_restr15.674
r_dihedral_angle_3_deg15.055
r_lrange_it8.565
r_scangle_it7.285
r_dihedral_angle_1_deg7.276
r_scbond_it5.762
r_mcangle_it3.786
r_mcbond_it3.268
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.067
r_dihedral_angle_4_deg18.889
r_rigid_bond_restr15.674
r_dihedral_angle_3_deg15.055
r_lrange_it8.565
r_scangle_it7.285
r_dihedral_angle_1_deg7.276
r_scbond_it5.762
r_mcangle_it3.786
r_mcbond_it3.268
r_angle_refined_deg1.895
r_nbtor_refined0.314
r_nbd_refined0.223
r_symmetry_nbd_refined0.201
r_symmetry_xyhbond_nbd_refined0.179
r_xyhbond_nbd_refined0.154
r_chiral_restr0.123
r_bond_refined_d0.012
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5993
Nucleic Acid Atoms
Solvent Atoms469
Heterogen Atoms150

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing