1S3T

BORATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2UBP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.32931.8 M AMS, 100 mM citric acid, 100 mM boric acid , pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.754.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.906α = 90
b = 130.906β = 90
c = 189.366γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHBent mirror2002-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.124.899.70.130.1313.98.1656339562152224.33
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1499.90.5470.5473.566.82104

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2ubp2.124.77548345483411411000.178050.178050.17750.20455RANDOM19.624
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]
1.310.651.31-1.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.281
r_scangle_it2.572
r_scbond_it1.528
r_angle_other_deg1.352
r_angle_refined_deg1.286
r_mcangle_it0.894
r_mcbond_it0.472
r_symmetry_vdw_other0.303
r_nbd_other0.243
r_symmetry_hbond_refined0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.281
r_scangle_it2.572
r_scbond_it1.528
r_angle_other_deg1.352
r_angle_refined_deg1.286
r_mcangle_it0.894
r_mcbond_it0.472
r_symmetry_vdw_other0.303
r_nbd_other0.243
r_symmetry_hbond_refined0.23
r_nbd_refined0.208
r_symmetry_vdw_refined0.194
r_xyhbond_nbd_refined0.136
r_nbtor_other0.084
r_chiral_restr0.077
r_gen_planes_other0.023
r_bond_other_d0.014
r_bond_refined_d0.012
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5959
Nucleic Acid Atoms
Solvent Atoms406
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing