7B5A

X-ray crystal structure of Sporosarcina pasteurii urease inhibited by Ag(PEt3)2NO3 determined at 1.97 Angstroms


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6G48 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293THE PROTEIN-LIGAND (300 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 coefficientSolvent content
2.7455.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.485α = 90
b = 131.485β = 90
c = 189.523γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-11-30MSINGLE 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
11.97113.871000.20.2340.0640.99812.213.26876229.2
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)
11.972.0299.93.1913.4730.9820.593112.4

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-VALUE6G481.9797.79868710334399.9530.1690.16680.209237.581
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]
1.5690.7841.569-5.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.793
r_dihedral_angle_4_deg17.73
r_dihedral_angle_3_deg14.512
r_dihedral_angle_1_deg7.705
r_lrange_it6.794
r_lrange_other6.685
r_scangle_it5.736
r_scangle_other5.283
r_scbond_it4.111
r_scbond_other3.819
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.793
r_dihedral_angle_4_deg17.73
r_dihedral_angle_3_deg14.512
r_dihedral_angle_1_deg7.705
r_lrange_it6.794
r_lrange_other6.685
r_scangle_it5.736
r_scangle_other5.283
r_scbond_it4.111
r_scbond_other3.819
r_mcangle_it3.664
r_mcangle_other3.664
r_mcbond_it2.882
r_mcbond_other2.881
r_angle_refined_deg1.756
r_angle_other_deg1.386
r_symmetry_nbd_refined0.225
r_nbd_refined0.206
r_nbd_other0.196
r_symmetry_nbd_other0.186
r_nbtor_refined0.16
r_xyhbond_nbd_refined0.16
r_symmetry_xyhbond_nbd_refined0.144
r_symmetry_xyhbond_nbd_other0.116
r_symmetry_nbtor_other0.086
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6047
Nucleic Acid Atoms
Solvent Atoms474
Heterogen Atoms107

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing