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EDTA-free crystal structure of the mutant C221D of 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 4.6 277 0.05 M sodium acetate, 0.05 M potassium phosphate monobasic, 20% PEG8000, 2 mM zinc chloride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.24 45.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.622 α = 90 b = 65.021 β = 90 c = 67.272 γ = 90
Symmetry Space Group P 21 21 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 2009-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.35 19.61 99.6 0.069 16.3 4.3 9845 33.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.48 98.6 0.264 5.2 4.2
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 (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 PDB ENTRY 1X8G 2.35 19.61 9802 9323 469 99 0.192 0.189 0.2106 0.261 0.2879 RANDOM 42.695
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] 3.62 -0.47 -3.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.273 r_dihedral_angle_4_deg 21.951 r_dihedral_angle_3_deg 15.242 r_dihedral_angle_1_deg 7.141 r_scangle_it 3.217 r_scbond_it 2.141 r_angle_refined_deg 1.707 r_mcangle_it 1.27 r_angle_other_deg 1.043 r_mcbond_it 0.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.273 r_dihedral_angle_4_deg 21.951 r_dihedral_angle_3_deg 15.242 r_dihedral_angle_1_deg 7.141 r_scangle_it 3.217 r_scbond_it 2.141 r_angle_refined_deg 1.707 r_mcangle_it 1.27 r_angle_other_deg 1.043 r_mcbond_it 0.746 r_mcbond_other 0.209 r_chiral_restr 0.102 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.001 r_bond_other_d 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 1613 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling