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Structure of IMP-13 metallo-beta-lactamase complexed with hydrolysed ertapenem
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R78
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M tri-Sodium acetate pH 5.6, 0.2 M Ammonium acetate, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.41 48.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.688 α = 90 b = 48.105 β = 105.73 c = 92.574 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M-F 2018-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.2 18.82 97.8 0.151 0.986 6.6 3.3 23338
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 94.7 1.002 0.397 3.2
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 (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 6R78 2.2 18.82 22254 1064 97.43 0.2017 0.2001 0.2029 0.2379 0.2372 RANDOM 37.358
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] -1.79 0.86 -1.39 2.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.769 r_dihedral_angle_3_deg 17.546 r_dihedral_angle_4_deg 10.274 r_dihedral_angle_1_deg 6.203 r_mcangle_it 3.917 r_mcbond_it 2.63 r_mcbond_other 2.611 r_angle_other_deg 2.346 r_angle_refined_deg 1.417 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.769 r_dihedral_angle_3_deg 17.546 r_dihedral_angle_4_deg 10.274 r_dihedral_angle_1_deg 6.203 r_mcangle_it 3.917 r_mcbond_it 2.63 r_mcbond_other 2.611 r_angle_other_deg 2.346 r_angle_refined_deg 1.417 r_chiral_restr 0.079 r_bond_other_d 0.035 r_bond_refined_d 0.009 r_gen_planes_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3438 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction