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Crystal structure of the zinc carbapenemase CPHA in complex with the inhibitor pyridine-2,4-dicarboxylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X8H PDB ENTRY 1X8H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 280 PEG, AS, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.638 α = 90 b = 101.211 β = 90 c = 117.121 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 MARRESEARCH 2005-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.54179
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 1.86 50 99.4 0.07 0.07 7.4 6.4 21756 21647 2 2
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 1.86 1.91 97.3 0.179 0.179 4.1 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1X8H 1.86 21.9 2 21625 20495 1102 99.29 0.161 0.16084 0.15898 0.1739 0.19617 RANDOM 14.148
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] -0.21 0.48 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.922 r_dihedral_angle_4_deg 20.365 r_dihedral_angle_3_deg 14.122 r_dihedral_angle_1_deg 6.18 r_scangle_it 3.474 r_scbond_it 2.185 r_angle_refined_deg 1.365 r_angle_other_deg 1.218 r_mcangle_it 1.181 r_mcbond_it 0.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.922 r_dihedral_angle_4_deg 20.365 r_dihedral_angle_3_deg 14.122 r_dihedral_angle_1_deg 6.18 r_scangle_it 3.474 r_scbond_it 2.185 r_angle_refined_deg 1.365 r_angle_other_deg 1.218 r_mcangle_it 1.181 r_mcbond_it 0.758 r_nbd_refined 0.359 r_symmetry_vdw_other 0.263 r_nbd_other 0.205 r_mcbond_other 0.205 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.106 r_symmetry_vdw_refined 0.104 r_nbtor_other 0.088 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_bond_other_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1758 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 31
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling CCP4 model building REFMAC refinement CCP4 data scaling CCP4 phasing