6ZNY

1.50 A resolution 3-methylcatechol (3-methylbenzene-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
2.7755.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.577α = 90
b = 131.577β = 90
c = 189.365γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-07-13MSINGLE 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)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
11.5113.94999.70.1130.1210.0420.99918.815.415303915.9
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)
11.51.5399.12.3592.5260.90.6871.514.9

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-VALUE5G4H1.594.862153002768399.5720.1340.1330.152121.148
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]
0.7420.3710.742-2.406
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.393
r_dihedral_angle_4_deg18.228
r_dihedral_angle_3_deg12.308
r_dihedral_angle_1_deg6.959
r_lrange_it5.443
r_lrange_other5.259
r_scangle_it4.315
r_scangle_other4.174
r_scbond_it2.961
r_scbond_other2.846
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.393
r_dihedral_angle_4_deg18.228
r_dihedral_angle_3_deg12.308
r_dihedral_angle_1_deg6.959
r_lrange_it5.443
r_lrange_other5.259
r_scangle_it4.315
r_scangle_other4.174
r_scbond_it2.961
r_scbond_other2.846
r_mcangle_other2.071
r_mcangle_it2.07
r_angle_refined_deg1.755
r_angle_other_deg1.491
r_mcbond_it1.462
r_mcbond_other1.46
r_nbd_refined0.213
r_symmetry_nbd_refined0.2
r_nbd_other0.187
r_symmetry_nbd_other0.176
r_nbtor_refined0.163
r_xyhbond_nbd_refined0.158
r_symmetry_xyhbond_nbd_refined0.158
r_chiral_restr0.093
r_symmetry_nbtor_other0.081
r_symmetry_xyhbond_nbd_other0.074
r_bond_refined_d0.011
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 Atoms716
Heterogen Atoms169

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing