6ZO1

1.61 A resolution 3,5-dimethylcatechol (3,5-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
2.7655.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.566α = 90
b = 131.566β = 90
c = 188.919γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.966PETRA 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
11.6145.4999.80.0970.1090.050.99912.48.712390821.3
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)
11.611.6499.61.6591.8670.8450.611.58.9

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-VALUE5G4H1.6145.49123886622899.6370.1370.13570.15924.4
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]
0.7860.3930.786-2.549
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.941
r_dihedral_angle_4_deg18.715
r_dihedral_angle_3_deg12.753
r_dihedral_angle_1_deg6.976
r_lrange_it6.664
r_lrange_other6.664
r_scangle_it5.241
r_scangle_other4.719
r_scbond_it3.777
r_scbond_other3.268
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.941
r_dihedral_angle_4_deg18.715
r_dihedral_angle_3_deg12.753
r_dihedral_angle_1_deg6.976
r_lrange_it6.664
r_lrange_other6.664
r_scangle_it5.241
r_scangle_other4.719
r_scbond_it3.777
r_scbond_other3.268
r_mcangle_it2.419
r_mcangle_other2.419
r_angle_refined_deg1.822
r_mcbond_it1.765
r_mcbond_other1.765
r_angle_other_deg1.499
r_symmetry_nbd_refined0.257
r_nbd_refined0.213
r_nbd_other0.21
r_symmetry_xyhbond_nbd_refined0.184
r_symmetry_nbd_other0.183
r_xyhbond_nbd_refined0.17
r_nbtor_refined0.165
r_chiral_restr0.098
r_symmetry_xyhbond_nbd_other0.087
r_symmetry_nbtor_other0.084
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 Atoms6041
Nucleic Acid Atoms
Solvent Atoms567
Heterogen Atoms210

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing