7P7N

X-RAY CRYSTAL STRUCTURE OF SPOROSARCINA PASTEURII UREASE INHIBITED BY THE GOLD(I)-PHOSPHINE COMPOUND Au(PEt3)I DETERMINED AT 1.80 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
2.7755.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.645α = 90
b = 131.645β = 90
c = 189.2γ = 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
11.81141000.1420.1540.0420.9991713.28975925.26
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)
11.81.831002.32.4840.9310.6941.513.5

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-VALUE5ol41.872.90789704441999.9750.1560.1550.176331.017
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]
1.0020.5011.002-3.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.617
r_rigid_bond_restr21.785
r_dihedral_angle_4_deg17.946
r_dihedral_angle_3_deg14.048
r_lrange_it7.792
r_dihedral_angle_1_deg7.187
r_scangle_it5.945
r_scbond_it4.443
r_mcangle_it3.033
r_mcbond_it2.422
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.617
r_rigid_bond_restr21.785
r_dihedral_angle_4_deg17.946
r_dihedral_angle_3_deg14.048
r_lrange_it7.792
r_dihedral_angle_1_deg7.187
r_scangle_it5.945
r_scbond_it4.443
r_mcangle_it3.033
r_mcbond_it2.422
r_angle_refined_deg1.747
r_nbtor_refined0.308
r_nbd_refined0.216
r_symmetry_nbd_refined0.204
r_symmetry_xyhbond_nbd_refined0.198
r_xyhbond_nbd_refined0.154
r_chiral_restr0.116
r_bond_refined_d0.013
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5994
Nucleic Acid Atoms
Solvent Atoms549
Heterogen Atoms143

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing