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BORATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2UBP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 293 1.8 M AMS, 100 mM citric acid, 100 mM boric acid , pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.7 54.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.906 α = 90 b = 130.906 β = 90 c = 189.366 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH Bent mirror 2002-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8 EMBL/DESY, HAMBURG X13
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 24.8 99.7 0.13 0.13 13.9 8.16 56339 56215 2 2 24.33
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) Redundancy Number Unique Reflections (All) 1 2.1 2.14 99.9 0.547 0.547 3.56 6.8 2104
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2ubp 2.1 24.77 54834 54834 1141 100 0.17805 0.17805 0.1775 0.1877 0.20455 0.208 RANDOM 19.624
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] 1.31 0.65 1.31 -1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.281 r_scangle_it 2.572 r_scbond_it 1.528 r_angle_other_deg 1.352 r_angle_refined_deg 1.286 r_mcangle_it 0.894 r_mcbond_it 0.472 r_symmetry_vdw_other 0.303 r_nbd_other 0.243 r_symmetry_hbond_refined 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.281 r_scangle_it 2.572 r_scbond_it 1.528 r_angle_other_deg 1.352 r_angle_refined_deg 1.286 r_mcangle_it 0.894 r_mcbond_it 0.472 r_symmetry_vdw_other 0.303 r_nbd_other 0.243 r_symmetry_hbond_refined 0.23 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.136 r_nbtor_other 0.084 r_chiral_restr 0.077 r_gen_planes_other 0.023 r_bond_other_d 0.014 r_bond_refined_d 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5959 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing