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Crystal Structure of the Zinc Carbapenemase CphA in Complex with the Antibiotic Biapenem
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 6.5 280 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 = 42.836 α = 90 b = 101.513 β = 90 c = 117.364 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 2003-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 1.9 26.5 93.1 0.12 0.12 3.7 5.9 20636
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 1.9 1.96 99.9 0.29 0.29 2.1 5.2
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 (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 1.9 26.5 19554 1051 99.94 0.153 0.15311 0.15147 0.1647 0.18308 0.1906 RANDOM 16.545
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] 0.35 -0.28 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.378 r_sphericity_bonded 4.489 r_scangle_it 4.224 r_sphericity_free 3.806 r_scbond_it 2.574 r_angle_refined_deg 1.748 r_mcangle_it 1.461 r_angle_other_deg 0.95 r_mcbond_it 0.815 r_symmetry_vdw_other 0.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.378 r_sphericity_bonded 4.489 r_scangle_it 4.224 r_sphericity_free 3.806 r_scbond_it 2.574 r_angle_refined_deg 1.748 r_mcangle_it 1.461 r_angle_other_deg 0.95 r_mcbond_it 0.815 r_symmetry_vdw_other 0.376 r_nbd_refined 0.375 r_nbd_other 0.246 r_symmetry_vdw_refined 0.215 r_xyhbond_nbd_refined 0.181 r_symmetry_hbond_refined 0.164 r_chiral_restr 0.098 r_nbtor_other 0.083 r_bond_refined_d 0.017 r_gen_planes_other 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1754 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 62
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling CCP4 model building REFMAC refinement CCP4 data scaling CCP4 phasing