6RP1

1.49 A RESOLUTION OF SPOROSARCINA PASTEURII UREASE INHIBITED IN THE PRESENCE OF NBPTO AT pH 6.5


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293Protein dissolved in 50 mM HEPES, pH 7.5, 2 mM EDTA, 4 mM NBPTO. Precipitant solution consisting of 100 mM citrate buffer, 1.7-1.9 M ammonium sulfate, 4 mM NBPTO, at pH 6.5.
Crystal Properties
Matthews coefficientSolvent content
2.7555.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.813α = 90
b = 131.813β = 90
c = 189.028γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9797PETRA 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
11.49114.1599.80.1230.1330.0360.99915.313.215661813.3
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)
11.491.5299.41.9332.1150.6070.5751.511.8

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 REPLACEMENTTHROUGHOUT5OL41.49114.15148730785999.740.137020.136190.15302RANDOM19.406
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]
0.540.270.54-1.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.392
r_dihedral_angle_4_deg17.889
r_dihedral_angle_3_deg11.749
r_dihedral_angle_1_deg6.047
r_long_range_B_refined5.307
r_long_range_B_other5.306
r_scangle_other2.941
r_scbond_it1.878
r_scbond_other1.878
r_mcangle_it1.532
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.392
r_dihedral_angle_4_deg17.889
r_dihedral_angle_3_deg11.749
r_dihedral_angle_1_deg6.047
r_long_range_B_refined5.307
r_long_range_B_other5.306
r_scangle_other2.941
r_scbond_it1.878
r_scbond_other1.878
r_mcangle_it1.532
r_mcangle_other1.532
r_angle_refined_deg1.442
r_mcbond_it0.991
r_mcbond_other0.989
r_angle_other_deg0.8
r_chiral_restr0.088
r_bond_refined_d0.01
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
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 Atoms709
Heterogen Atoms97

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing