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Structure of beta-lactamase II from Bacillus cereus. R121H, C221S double mutant. Space group P3121.
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 4.9 295 0.1 M sodium acetate, 2.8 M ammonium sulfate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.31 46.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.665 α = 90 b = 66.665 β = 90 c = 175.947 γ = 120
Symmetry Space Group P 31 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 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 1.8 50 94.8 0.061 11.6 5.2 40696 202606
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 1.8 1.86 91.9 0.45 3.8 5
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 1.8 58.62 40696 2060 94.92 0.177 0.175 0.1738 0.217 0.2173 RANDOM 23.194
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] 0.15 0.08 0.15 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.061 r_dihedral_angle_4_deg 15.435 r_dihedral_angle_3_deg 13.066 r_dihedral_angle_1_deg 6.452 r_scangle_it 3.776 r_scbond_it 2.363 r_mcangle_it 1.577 r_angle_refined_deg 1.455 r_mcbond_it 0.948 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.061 r_dihedral_angle_4_deg 15.435 r_dihedral_angle_3_deg 13.066 r_dihedral_angle_1_deg 6.452 r_scangle_it 3.776 r_scbond_it 2.363 r_mcangle_it 1.577 r_angle_refined_deg 1.455 r_mcbond_it 0.948 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.14 r_metal_ion_refined 0.133 r_symmetry_hbond_refined 0.12 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3346 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing