6ZO0

2.23 A resolution 3,4-dimethylcatechol (3,4-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
2.7555.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.501α = 90
b = 131.501β = 90
c = 188.71γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.000ELETTRA11.2C

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
12.23188.711000.2710.2990.1250.995910.74758527.9
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)
12.232.31001.7511.9290.8040.6571.511

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-VALUE5G4H2.23113.88347536227999.9710.1640.16110.216234.357
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]
1.0380.5191.038-3.368
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.16
r_dihedral_angle_4_deg19.595
r_dihedral_angle_3_deg16.035
r_lrange_it9.216
r_dihedral_angle_1_deg7.57
r_scangle_it6.299
r_scbond_it4.562
r_mcangle_it3.808
r_mcbond_it2.757
r_angle_refined_deg1.861
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.16
r_dihedral_angle_4_deg19.595
r_dihedral_angle_3_deg16.035
r_lrange_it9.216
r_dihedral_angle_1_deg7.57
r_scangle_it6.299
r_scbond_it4.562
r_mcangle_it3.808
r_mcbond_it2.757
r_angle_refined_deg1.861
r_nbtor_refined0.317
r_nbd_refined0.227
r_symmetry_nbd_refined0.198
r_symmetry_xyhbond_nbd_refined0.186
r_xyhbond_nbd_refined0.178
r_chiral_restr0.122
r_bond_refined_d0.009
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6041
Nucleic Acid Atoms
Solvent Atoms394
Heterogen Atoms152

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing