8A18

1.63 A resolution hydroquinone inhibited Sporosarcina pasteurii urease


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5G4H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293THE PROTEIN-LIGAND (1 mM) COMPLEX IN 50 MM HEPES BUFFER, PH 7.50, DILUTED 1:1 WITH A SOLUTION OF 1.6-2.0 M AMMONIUM SULFATE in 100 mM citrate buffer at pH 6.3
Crystal Properties
Matthews coefficientSolvent content
2.6353.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.666α = 90
b = 131.666β = 90
c = 189.129γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2022-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9537PETRA 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)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
11.631151000.120.1270.04319.916.3120118
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.631.661001.992.1420.7861.514.1

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-VALUE5G4H1.63114.287120090596899.8640.1290.12790.15822.827
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]
0.680.340.68-2.204
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.016
r_dihedral_angle_4_deg18.179
r_dihedral_angle_3_deg12.492
r_dihedral_angle_other_3_deg11.858
r_lrange_it7.294
r_lrange_other7.151
r_dihedral_angle_1_deg6.92
r_scangle_it4.886
r_scangle_other4.487
r_scbond_it3.392
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.016
r_dihedral_angle_4_deg18.179
r_dihedral_angle_3_deg12.492
r_dihedral_angle_other_3_deg11.858
r_lrange_it7.294
r_lrange_other7.151
r_dihedral_angle_1_deg6.92
r_scangle_it4.886
r_scangle_other4.487
r_scbond_it3.392
r_scbond_other3.059
r_mcangle_other2.297
r_mcangle_it2.296
r_angle_refined_deg1.851
r_mcbond_it1.685
r_mcbond_other1.682
r_angle_other_deg1.5
r_nbd_refined0.237
r_nbd_other0.226
r_symmetry_nbd_refined0.222
r_symmetry_xyhbond_nbd_refined0.21
r_symmetry_nbd_other0.181
r_xyhbond_nbd_refined0.165
r_nbtor_refined0.163
r_chiral_restr0.099
r_symmetry_nbtor_other0.081
r_symmetry_xyhbond_nbd_other0.077
r_xyhbond_nbd_other0.035
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6046
Nucleic Acid Atoms
Solvent Atoms667
Heterogen Atoms184

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing