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Structure of IMP-13 metallo-beta-lactamase complexed with hydrolysed doripenem
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Sodium HEPES pH 7.5, 25% PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.69 54.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.43 α = 90 b = 72.318 β = 111.72 c = 62.933 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 2018-12-06 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 2.84 45.51 98.84 0.998 11.57 6.8 82215 12023
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 2.84 2.95 0.626
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.85 45.51 11394 632 99.23 0.2301 0.2284 0.2282 0.2626 0.2653 RANDOM 68.872
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] 1.62 -7.74 8.25 -2.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.593 r_dihedral_angle_3_deg 18.142 r_dihedral_angle_4_deg 12.385 r_mcangle_it 7.238 r_dihedral_angle_1_deg 7.136 r_mcbond_it 4.618 r_mcbond_other 4.611 r_angle_other_deg 2.353 r_angle_refined_deg 1.593 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.593 r_dihedral_angle_3_deg 18.142 r_dihedral_angle_4_deg 12.385 r_mcangle_it 7.238 r_dihedral_angle_1_deg 7.136 r_mcbond_it 4.618 r_mcbond_other 4.611 r_angle_other_deg 2.353 r_angle_refined_deg 1.593 r_chiral_restr 0.087 r_bond_other_d 0.035 r_gen_planes_other 0.009 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3408 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction