4UBP | pdb_00004ubp

STRUCTURE OF BACILLUS PASTEURII UREASE INHIBITED WITH ACETOHYDROXAMIC ACID AT 1.55 A RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.3ATED AMMONIUM SULPHATE, 1.2 M LICL), DROXAMIC ACID, 1OOMM SODIUM CITRATE PH 6.3. HANGING DROP 20 C, 3 UL PROTEIN SOLUTION (11 MG/ML IN 20 MM TRIS HCL PH 8.0 + 4MM ACETOHYDROXAMIC ACID) + 3 MICROLITERS PRECIPITANT SOLUTION, pH 6.30
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.88α = 90
b = 130.88β = 90
c = 189γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHBENT MIRROR1998-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

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
11.553599.50.0710.07115.0326.02138830-3
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)
11.551.5899.90.4790.4792.234.29

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTRFREE2UBP1.5532.73136971275499.50.15130.15130.170.19RANDOM26.22
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]
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor30.9
p_staggered_tor13.2
p_planar_tor5.1
p_scangle_it3.984
p_scbond_it2.977
p_mcangle_it2.957
p_mcbond_it2.251
p_multtor_nbd0.254
p_singtor_nbd0.175
p_planar_d0.038
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor30.9
p_staggered_tor13.2
p_planar_tor5.1
p_scangle_it3.984
p_scbond_it2.977
p_mcangle_it2.957
p_mcbond_it2.251
p_multtor_nbd0.254
p_singtor_nbd0.175
p_planar_d0.038
p_angle_d0.03
p_bond_d0.013
p_angle_deg
p_hb_or_metal_coord
p_plane_restr
p_chiral_restr
p_xhyhbond_nbd
p_xyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6056
Nucleic Acid Atoms
Solvent Atoms746
Heterogen Atoms7

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement