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Crystal Structure of the Mono-Zinc Carbapenemase CphA from Aeromonas Hydrophyla
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X8H CphA (N220G mutant)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 278 PEG, AS, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.628 α = 90 b = 101.205 β = 90 c = 118.239 γ = 90
Symmetry Space Group C 2 2 21
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 2003-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979469 ESRF BM30A
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 1.7 58.722 94.7 0.123 0.123 3.9 3.5 27567
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 1.7 1.79 94.7 0.312 0.312 2.8 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 (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 CphA (N220G mutant) 1.7 25 25532 1370 94.04 0.184 0.18401 0.18306 0.1878 0.20118 0.2067 RANDOM 14.394
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] -0.55 0.56
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 8.133 r_dihedral_angle_1_deg 6.733 r_sphericity_bonded 5.079 r_scangle_it 4.114 r_scbond_it 2.483 r_angle_refined_deg 1.629 r_mcangle_it 1.478 r_angle_other_deg 0.914 r_mcbond_it 0.907 r_nbd_refined 0.385
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 8.133 r_dihedral_angle_1_deg 6.733 r_sphericity_bonded 5.079 r_scangle_it 4.114 r_scbond_it 2.483 r_angle_refined_deg 1.629 r_mcangle_it 1.478 r_angle_other_deg 0.914 r_mcbond_it 0.907 r_nbd_refined 0.385 r_symmetry_vdw_other 0.332 r_nbd_other 0.24 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.16 r_symmetry_vdw_refined 0.108 r_chiral_restr 0.105 r_nbtor_other 0.083 r_metal_ion_refined 0.044 r_bond_refined_d 0.017 r_gen_planes_other 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1758 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 10
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling CCP4 model building REFMAC refinement CCP4 data scaling CCP4 phasing