5G4H

1.50 A resolution catechol (1,2-dihydroxybenzene) inhibited Sporosarcina pasteurii urease


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AC7PDB ENTRY 4AC7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.31.8 M AMMONIUM SULFATE, 50 MM SODIUM CITRATE BUFFER, PH 6.3
Crystal Properties
Matthews coefficientSolvent content
2.7555.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.276α = 90
b = 131.276β = 90
c = 189.017γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.594.511000.0723.111.81527221.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5399.91.311.69.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4AC71.5113.69144972766299.960.122850.121180.15423RANDOM23.351
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]
1.050.531.05-3.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.653
r_sphericity_free34.259
r_dihedral_angle_4_deg16.573
r_sphericity_bonded11.931
r_dihedral_angle_3_deg11.67
r_dihedral_angle_1_deg6.16
r_scbond_it3.402
r_mcangle_it2.248
r_rigid_bond_restr2.15
r_mcbond_it1.958
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.653
r_sphericity_free34.259
r_dihedral_angle_4_deg16.573
r_sphericity_bonded11.931
r_dihedral_angle_3_deg11.67
r_dihedral_angle_1_deg6.16
r_scbond_it3.402
r_mcangle_it2.248
r_rigid_bond_restr2.15
r_mcbond_it1.958
r_mcbond_other1.957
r_angle_refined_deg1.369
r_angle_other_deg0.778
r_chiral_restr0.081
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6044
Nucleic Acid Atoms
Solvent Atoms675
Heterogen Atoms101

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
CCP4phasing