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Structure of IMP-13 metallo-beta-lactamase in apo form (loop open)
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 298 0.1 M Tris pH 8.5, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.43 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.762 α = 107.52 b = 64.825 β = 90.99 c = 86.546 γ = 94.8
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 193 PIXEL DECTRIS PILATUS3 6M 2018-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9660 ESRF ID30B
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 61.55 94.65 0.997 9.58 1.7 67023
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.968
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 FREE R-VALUE 6R78 1.9 61.55 65582 3373 94.75 0.1772 0.1753 0.2139 0.2153 RANDOM 29.658
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] 1.05 -1.89 -2.16 0.23 0.91 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.583 r_dihedral_angle_4_deg 13.434 r_dihedral_angle_3_deg 13.218 r_dihedral_angle_1_deg 6.994 r_angle_refined_deg 1.389 r_angle_other_deg 1.326 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.583 r_dihedral_angle_4_deg 13.434 r_dihedral_angle_3_deg 13.218 r_dihedral_angle_1_deg 6.994 r_angle_refined_deg 1.389 r_angle_other_deg 1.326 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6730 Nucleic Acid Atoms Solvent Atoms 901 Heterogen Atoms 139
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction