6ZO2

1.65 A resolution 4,5-dimethylcatechol (4,5-dimethylbenzene-1,2-diol) 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 DROP6.329350 mM citrate buffer at pH 6.3, containing 1.6 - 2.0 M ammonium sulfate as a precipitant
Crystal Properties
Matthews coefficientSolvent content
2.7755.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.64α = 90
b = 131.64β = 90
c = 189.254γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2018-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.96769ESRFID30B

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
11.6562.2451000.1310.1370.0420.99918.620.511604120.6
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)
11.651.681002.8112.9470.8830.7711.521.2

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-VALUE5G4H1.6562.24115979581399.9740.1360.13440.155624.979
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]
0.7290.3650.729-2.366
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.325
r_dihedral_angle_4_deg17.885
r_dihedral_angle_3_deg12.236
r_dihedral_angle_1_deg7.018
r_lrange_it6.338
r_lrange_other6.338
r_scangle_it4.819
r_scangle_other4.403
r_scbond_it3.261
r_scbond_other3.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.325
r_dihedral_angle_4_deg17.885
r_dihedral_angle_3_deg12.236
r_dihedral_angle_1_deg7.018
r_lrange_it6.338
r_lrange_other6.338
r_scangle_it4.819
r_scangle_other4.403
r_scbond_it3.261
r_scbond_other3.015
r_mcangle_it2.278
r_mcangle_other2.278
r_angle_refined_deg1.745
r_mcbond_it1.666
r_mcbond_other1.664
r_angle_other_deg1.475
r_symmetry_nbd_refined0.218
r_nbd_refined0.211
r_nbd_other0.206
r_symmetry_nbd_other0.18
r_nbtor_refined0.162
r_symmetry_xyhbond_nbd_refined0.158
r_xyhbond_nbd_refined0.154
r_symmetry_xyhbond_nbd_other0.137
r_chiral_restr0.093
r_symmetry_nbtor_other0.085
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6041
Nucleic Acid Atoms
Solvent Atoms648
Heterogen Atoms170

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing