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Structure of IMP-13 metallo-beta-lactamase complexed with citrate anion
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 Ammonium acetate, Na citrate, PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.49 50.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.675 α = 90 b = 90.467 β = 100.853 c = 88.522 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 90 PIXEL DECTRIS PILATUS 2M-F 2020-02-09 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 1.7 46.866 99.74 0.998 6.4 5.7 80810
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 1.7 1.76 0.72
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6R78 1.7 46.866 80810 3820 99.719 0.182 0.18 0.18 0.2129 0.2128 30.136
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] -0.139 -0.443 1.654 -1.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.901 r_dihedral_angle_3_deg 15.744 r_dihedral_angle_4_deg 14.311 r_lrange_it 7.045 r_lrange_other 6.995 r_dihedral_angle_1_deg 6.818 r_scangle_it 5.464 r_scangle_other 5.464 r_mcangle_other 3.841 r_mcangle_it 3.839
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.901 r_dihedral_angle_3_deg 15.744 r_dihedral_angle_4_deg 14.311 r_lrange_it 7.045 r_lrange_other 6.995 r_dihedral_angle_1_deg 6.818 r_scangle_it 5.464 r_scangle_other 5.464 r_mcangle_other 3.841 r_mcangle_it 3.839 r_scbond_it 3.67 r_scbond_other 3.67 r_mcbond_it 2.833 r_mcbond_other 2.826 r_angle_other_deg 2.342 r_angle_refined_deg 1.67 r_symmetry_xyhbond_nbd_other 0.477 r_symmetry_xyhbond_nbd_refined 0.357 r_metal_ion_refined 0.269 r_nbd_other 0.258 r_nbd_refined 0.232 r_symmetry_nbd_other 0.222 r_xyhbond_nbd_refined 0.222 r_symmetry_nbd_refined 0.195 r_nbtor_refined 0.167 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.076 r_bond_other_d 0.035 r_gen_planes_other 0.014 r_bond_refined_d 0.011 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5139 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing