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Structure of Zn-dependent Metallo-Beta-Lactamase from Bacillus Cereus R121H, C221D Double Mutant
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, pH 5.4, 60 mM sodium tartrate, 18% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.26 45.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.471 α = 90 b = 61.008 β = 92.85 c = 68.674 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 1.42 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 50 94.5 0.073 12 3.4 9218 29486
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.38 70.7 0.24 3 2
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 2.29 68.52 9218 440 94.01 0.167 0.163 0.1622 0.256 0.2539 RANDOM 25.606
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] -0.02 -0.68 0.74 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.988 r_dihedral_angle_4_deg 17.721 r_dihedral_angle_3_deg 16.614 r_dihedral_angle_1_deg 7.456 r_scangle_it 4.841 r_scbond_it 3.099 r_mcangle_it 1.967 r_angle_refined_deg 1.96 r_mcbond_it 1.153 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.988 r_dihedral_angle_4_deg 17.721 r_dihedral_angle_3_deg 16.614 r_dihedral_angle_1_deg 7.456 r_scangle_it 4.841 r_scbond_it 3.099 r_mcangle_it 1.967 r_angle_refined_deg 1.96 r_mcbond_it 1.153 r_nbtor_refined 0.313 r_symmetry_hbond_refined 0.28 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.218 r_chiral_restr 0.126 r_bond_refined_d 0.022 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1668 Nucleic Acid Atoms Solvent Atoms 143 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