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Structure of beta-lactamase II from Bacillus cereus. R121H, C221D doble mutant with two zinc ions.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BC2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 295 0.1 M sodium cacodylate,60 mM sodium tartrate, 18% PEG 3350, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.26 45.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.464 α = 90 b = 61.023 β = 92.92 c = 68.71 γ = 90
Symmetry Space Group C 1 2 1
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 MAR CCD 165 mm 2006-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.42 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.84 50 97.6 0.047 12.4 2.6 18461 45536
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.84 1.91 86.3 0.277 2.9 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1bc2 1.84 68.68 18461 947 97.87 0.182 0.179 0.1772 0.241 0.2375 RANDOM 23.794
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] -0.89 0.52 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.195 r_dihedral_angle_4_deg 20.016 r_dihedral_angle_3_deg 13.09 r_dihedral_angle_1_deg 6.415 r_scangle_it 3.748 r_scbond_it 2.421 r_mcangle_it 1.584 r_angle_refined_deg 1.566 r_mcbond_it 0.986 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.195 r_dihedral_angle_4_deg 20.016 r_dihedral_angle_3_deg 13.09 r_dihedral_angle_1_deg 6.415 r_scangle_it 3.748 r_scbond_it 2.421 r_mcangle_it 1.584 r_angle_refined_deg 1.566 r_mcbond_it 0.986 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.171 r_symmetry_hbond_refined 0.166 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_metal_ion_refined 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1668 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing