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Crystal Structure of the Di-Zinc Carbapenemase CphA from Aeromonas Hydrophila
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X8G PDB ENTRY 1X8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 2.4M (NH4)2SO4, 100mM MES, 100mM ZnCl2, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 50.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.8 α = 90 b = 101.05 β = 90 c = 116.49 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 IMAGE PLATE MAR scanner 345 mm plate mirror 2007-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5418
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 2.03 19.71 99.7 0.062 34.4 14 16773 16754 15.64
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) 1 2.03 2.14 98.5 0.161 17.6 13.3 2365
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MIR THROUGHOUT PDB ENTRY 1X8G 2.03 14.56 16773 15863 845 99.73 0.15886 0.15886 0.15668 0.17 0.20203 0.2157 RANDOM 9.812
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] 0.03 -0.05 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.766 r_dihedral_angle_4_deg 15.725 r_dihedral_angle_3_deg 12.973 r_dihedral_angle_1_deg 6.199 r_scangle_it 2.142 r_scbond_it 1.561 r_angle_refined_deg 1.217 r_angle_other_deg 0.836 r_mcangle_it 0.694 r_mcbond_it 0.408
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.766 r_dihedral_angle_4_deg 15.725 r_dihedral_angle_3_deg 12.973 r_dihedral_angle_1_deg 6.199 r_scangle_it 2.142 r_scbond_it 1.561 r_angle_refined_deg 1.217 r_angle_other_deg 0.836 r_mcangle_it 0.694 r_mcbond_it 0.408 r_mcbond_other 0.106 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1763 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 37
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling