5OL4

1.28 A resolution of Sporosarcina pasteurii urease inhibited in the presence of NBPT


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UBP 

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
2.7655.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.742α = 90
b = 131.742β = 90
c = 188.93γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.934PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.28114.0999.40.1170.0330.99915.914.324393910.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.281.398.12.20.6250.6731.514.6

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 REPLACEMENTTHROUGHOUT3UBP1.28114.092316541224699.260.119920.119030.13684RANDOM14.901
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]
0.230.120.23-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.359
r_sphericity_free26.481
r_dihedral_angle_4_deg17.406
r_dihedral_angle_3_deg11.775
r_rigid_bond_restr8.153
r_sphericity_bonded6.804
r_dihedral_angle_1_deg6.149
r_long_range_B_refined2.567
r_long_range_B_other2.567
r_scangle_other1.935
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.359
r_sphericity_free26.481
r_dihedral_angle_4_deg17.406
r_dihedral_angle_3_deg11.775
r_rigid_bond_restr8.153
r_sphericity_bonded6.804
r_dihedral_angle_1_deg6.149
r_long_range_B_refined2.567
r_long_range_B_other2.567
r_scangle_other1.935
r_scbond_it1.547
r_scbond_other1.547
r_angle_refined_deg1.377
r_mcangle_it0.928
r_mcangle_other0.928
r_angle_other_deg0.808
r_mcbond_it0.685
r_mcbond_other0.685
r_chiral_restr0.085
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6046
Nucleic Acid Atoms
Solvent Atoms782
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing