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Crystal Structure of Active Site Influencing Variant (F218Y) of Imp-1 Metallo-beta-lactamase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DDK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 0.2M Sodium Acetate, 0.1M Sodium Citrate, 34% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.9 57.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.418 α = 90 b = 49.301 β = 92.348 c = 110.696 γ = 90
Symmetry Space Group I 1 2 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 RIGAKU HyPix-6000HE 2023-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.9 24.682 99.7 0.132 0.14 0.047 0.998 17.1 16.3 12578
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.08 0.547 0.59 0.218 0.974 13.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.9 24.682 12357 550 97.932 0.212 0.2095 0.2503 0.2715 0.3107 28.772
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] 1.956 1.202 -8.027 5.952
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 23.091 r_dihedral_angle_3_deg 18.604 r_dihedral_angle_6_deg 13.502 r_dihedral_angle_2_deg 10.109 r_scangle_it 9.396 r_dihedral_angle_1_deg 8.906 r_mcangle_it 8.47 r_scbond_it 6.046 r_mcbond_it 5.191 r_rigid_bond_restr 3.385
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 23.091 r_dihedral_angle_3_deg 18.604 r_dihedral_angle_6_deg 13.502 r_dihedral_angle_2_deg 10.109 r_scangle_it 9.396 r_dihedral_angle_1_deg 8.906 r_mcangle_it 8.47 r_scbond_it 6.046 r_mcbond_it 5.191 r_rigid_bond_restr 3.385 r_angle_refined_deg 1.898 r_symmetry_nbd_refined 0.536 r_nbtor_refined 0.317 r_nbd_refined 0.259 r_xyhbond_nbd_refined 0.21 r_symmetry_xyhbond_nbd_refined 0.193 r_chiral_restr 0.132 r_metal_ion_refined 0.124 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3425 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement CrysalisPro data collection CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing