6ZNZ

1.89 A resolution 4-methylcatechol (4-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
2.7455.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.021α = 90
b = 131.021β = 90
c = 188.879γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-06-10MSINGLE 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
11.8997.2799.80.1240.1590.0980.9949.54.47669117.2
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)
11.891.9399.80.8421.0990.6980.6751.54.1

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-VALUE5G4H1.8997.2776656377999.7090.160.15910.178127.624
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]
1.1810.5911.181-3.831
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.681
r_dihedral_angle_4_deg18.688
r_dihedral_angle_3_deg13.708
r_dihedral_angle_1_deg7.236
r_lrange_it6.548
r_scangle_it4.853
r_scbond_it3.534
r_mcangle_it2.594
r_mcbond_it1.943
r_angle_refined_deg1.653
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.681
r_dihedral_angle_4_deg18.688
r_dihedral_angle_3_deg13.708
r_dihedral_angle_1_deg7.236
r_lrange_it6.548
r_scangle_it4.853
r_scbond_it3.534
r_mcangle_it2.594
r_mcbond_it1.943
r_angle_refined_deg1.653
r_nbtor_refined0.306
r_nbd_refined0.214
r_symmetry_nbd_refined0.197
r_symmetry_xyhbond_nbd_refined0.163
r_xyhbond_nbd_refined0.147
r_chiral_restr0.105
r_bond_refined_d0.01
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6040
Nucleic Acid Atoms
Solvent Atoms584
Heterogen Atoms171

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing