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Structure of IMP-13 metallo-beta-lactamase complexed with hydrolysed imipenem
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R79
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M Bis-Tris pH 5.5, 0.2 M Ammonium sulfate, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.72 54.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.207 α = 90 b = 90.925 β = 90 c = 120.811 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 PIXEL DECTRIS PILATUS 2M-F 2019-02-11 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) 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 1.9 45.5 99.24 0.99 11.65 6.6 42307 37.72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.96 0.75
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6R79 1.9 45.5 40169 2138 99.25 0.1909 0.1889 0.2276 0.2473 RANDOM 45.296
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] 3.93 -1.42 -2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.049 r_dihedral_angle_4_deg 22.406 r_dihedral_angle_3_deg 15.779 r_dihedral_angle_1_deg 6.758 r_mcangle_it 4.846 r_mcbond_it 3.874 r_mcbond_other 3.865 r_angle_other_deg 2.28 r_angle_refined_deg 1.464 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.049 r_dihedral_angle_4_deg 22.406 r_dihedral_angle_3_deg 15.779 r_dihedral_angle_1_deg 6.758 r_mcangle_it 4.846 r_mcbond_it 3.874 r_mcbond_other 3.865 r_angle_other_deg 2.28 r_angle_refined_deg 1.464 r_chiral_restr 0.071 r_bond_other_d 0.035 r_bond_refined_d 0.01 r_gen_planes_other 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3438 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction