6H8J

1.45 A resolution of Sporosarcina pasteurii urease inhibited in the presence of NBPTO


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OL4 

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
2.7555.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.446α = 90
b = 131.446β = 90
c = 188.716γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2018-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.967700ESRFID30B

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
11.4548.7499.10.1070.0310.99916.213.8168094
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)
11.451.4797.91.940.5780.6551.512.8

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 REPLACEMENTTHROUGHOUT5OL41.4548.74159601844699.470.12530.124340.14316RANDOM18.867
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]
0.570.290.57-1.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.755
r_sphericity_free20.347
r_dihedral_angle_4_deg18.271
r_dihedral_angle_3_deg12.283
r_dihedral_angle_1_deg6.119
r_sphericity_bonded4.982
r_long_range_B_refined2.322
r_long_range_B_other2.305
r_scangle_other2.247
r_rigid_bond_restr2.195
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.755
r_sphericity_free20.347
r_dihedral_angle_4_deg18.271
r_dihedral_angle_3_deg12.283
r_dihedral_angle_1_deg6.119
r_sphericity_bonded4.982
r_long_range_B_refined2.322
r_long_range_B_other2.305
r_scangle_other2.247
r_rigid_bond_restr2.195
r_scbond_it1.902
r_scbond_other1.901
r_angle_refined_deg1.356
r_mcangle_it1.294
r_mcangle_other1.294
r_mcbond_it1.081
r_mcbond_other1.081
r_angle_other_deg0.787
r_chiral_restr0.08
r_bond_refined_d0.007
r_gen_planes_refined0.007
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6047
Nucleic Acid Atoms
Solvent Atoms626
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing