4AC7

The crystal structure of Sporosarcina pasteurii urease in complex with citrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S3TPDB ENTRY 1S3T DEPLETED OF WATERS SULPHATES AND BORATE WAS USED AS A MODEL FOR RIGID BODY REFINEMENT FOLLOWED BY REFINEMENT AND MODEL BUILDING

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.31.8 M AMMONIUM SULPHATE, 100 MM CITRATE PH 6.3, 50 MM NA2SO3
Crystal Properties
Matthews coefficientSolvent content
2.7655.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.555α = 90
b = 131.555β = 90
c = 189.521γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2011-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)PETRA III, EMBL c/o DESYP14 (MX2)

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
11.5113.9399.90.122.615.51537382
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)
11.51.581000.5849.9

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1S3T DEPLETED OF WATERS SULPHATES AND BORATE WAS USED AS A MODEL FOR RIGID BODY REFINEMENT FOLLOWED BY REFINEMENT AND MODEL BUILDING1.5113.93145792771299.860.118470.117030.14605RANDOM13.109
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]
0.520.260.52-0.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.847
r_sphericity_free24.641
r_dihedral_angle_4_deg16.322
r_dihedral_angle_3_deg11.53
r_sphericity_bonded7.086
r_dihedral_angle_1_deg6.259
r_rigid_bond_restr2.383
r_angle_refined_deg1.448
r_angle_other_deg0.947
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.847
r_sphericity_free24.641
r_dihedral_angle_4_deg16.322
r_dihedral_angle_3_deg11.53
r_sphericity_bonded7.086
r_dihedral_angle_1_deg6.259
r_rigid_bond_restr2.383
r_angle_refined_deg1.448
r_angle_other_deg0.947
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
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 Atoms6014
Nucleic Acid Atoms
Solvent Atoms671
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing