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Structure of beta-lactamase II from Bacillus cereus. R121H, C221S double mutant. Space group C2.
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 2.27 45.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.587 α = 90 b = 61.156 β = 93.11 c = 68.634 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 2006-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 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 2.28 50 98.3 0.059 14.8 6.4 9968
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) 2.28 2.35 83 0.17 9.7 2.8
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 2.28 68.52 9968 478 99.75 0.167 0.163 0.1625 0.238 0.2365 RANDOM 24.092
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] -0.42 -0.72 0.62 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.114 r_dihedral_angle_4_deg 18.471 r_dihedral_angle_3_deg 15.974 r_dihedral_angle_1_deg 7.322 r_scangle_it 4.835 r_scbond_it 3.045 r_angle_refined_deg 2.034 r_mcangle_it 1.876 r_mcbond_it 1.075 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.114 r_dihedral_angle_4_deg 18.471 r_dihedral_angle_3_deg 15.974 r_dihedral_angle_1_deg 7.322 r_scangle_it 4.835 r_scbond_it 3.045 r_angle_refined_deg 2.034 r_mcangle_it 1.876 r_mcbond_it 1.075 r_nbtor_refined 0.315 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.214 r_xyhbond_nbd_refined 0.181 r_symmetry_hbond_refined 0.156 r_chiral_restr 0.127 r_metal_ion_refined 0.04 r_bond_refined_d 0.021 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1666 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing