7ZCY

Sporosarcina pasteurii urease (SPU) co-crystallized in the presence of an Ebselen-derivative and bound to Se atoms


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5G4H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1COUNTER-DIFFUSION6.3293Protein-ligand (1 mM ligand concentration) complex in 50 mM HEPES buffer, pH 7.50 (also containing 10% (V/V) DMSO), diluted 1:1 with 1.6-2.1 M ammonium sulfate also containing 100 mM sodium citrate at pH 6.3
Crystal Properties
Matthews coefficientSolvent content
2.7254.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.612α = 90
b = 131.612β = 90
c = 189.003γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9763PETRA 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
11.541891000.0940.0990.031120.919.514203121.21
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)
11.541.571002.3012.4220.7520.7491.619.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5G4H1.5497.8134952701699.950.138570.137470.15991RANDOM25.426
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]
0.70.350.7-2.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.735
r_dihedral_angle_4_deg19.263
r_dihedral_angle_3_deg12.928
r_dihedral_angle_1_deg7.093
r_long_range_B_other5.923
r_long_range_B_refined5.922
r_scangle_other4.506
r_scbond_it3.237
r_scbond_other3.234
r_mcangle_it2.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.735
r_dihedral_angle_4_deg19.263
r_dihedral_angle_3_deg12.928
r_dihedral_angle_1_deg7.093
r_long_range_B_other5.923
r_long_range_B_refined5.922
r_scangle_other4.506
r_scbond_it3.237
r_scbond_other3.234
r_mcangle_it2.53
r_mcangle_other2.53
r_mcbond_it1.844
r_mcbond_other1.842
r_angle_refined_deg1.806
r_angle_other_deg1.5
r_chiral_restr0.099
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.003
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6046
Nucleic Acid Atoms
Solvent Atoms767
Heterogen Atoms143

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing