6ZO3

1.55 A resolution 3,6-dimethylcatechol (3,6-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
2.7655.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.463α = 90
b = 131.463β = 90
c = 189.067γ = 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 ID30B0.9677ESRFID30B

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
11.5548.7799.90.1270.1350.0460.99917.81613921513.2
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)
11.551.5897.52.1452.2880.7920.671.515.6

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-VALUE5G4H1.5547.311139006698399.9670.1360.13550.15620.213
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]
0.6810.340.681-2.209
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.199
r_dihedral_angle_4_deg18.057
r_dihedral_angle_3_deg12.389
r_dihedral_angle_1_deg7.01
r_lrange_it5.592
r_lrange_other5.592
r_scangle_it4.037
r_scangle_other3.827
r_scbond_it2.723
r_scbond_other2.581
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.199
r_dihedral_angle_4_deg18.057
r_dihedral_angle_3_deg12.389
r_dihedral_angle_1_deg7.01
r_lrange_it5.592
r_lrange_other5.592
r_scangle_it4.037
r_scangle_other3.827
r_scbond_it2.723
r_scbond_other2.581
r_mcangle_it1.943
r_mcangle_other1.943
r_angle_refined_deg1.765
r_angle_other_deg1.507
r_mcbond_it1.408
r_mcbond_other1.408
r_symmetry_nbd_refined0.226
r_nbd_refined0.223
r_nbd_other0.207
r_symmetry_nbd_other0.189
r_nbtor_refined0.164
r_xyhbond_nbd_refined0.155
r_symmetry_xyhbond_nbd_refined0.154
r_symmetry_xyhbond_nbd_other0.105
r_symmetry_nbtor_other0.097
r_chiral_restr0.093
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 Atoms6034
Nucleic Acid Atoms
Solvent Atoms758
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing