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Crystal structure of IMP-1 metallo-beta-lactamase in complex with NO9 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EV6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30% PEG 3350, 0.2M sodium acetate, 0.1M HEPES
Crystal Properties Matthews coefficient Solvent content 2.03 39.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.92 α = 90 b = 56.61 β = 90 c = 100.62 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 CCD ADSC QUANTUM 315r 2017-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AichiSR BEAMLINE BL2S1 1.12 AichiSR BL2S1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.68 56.61 99.7 0.067 18.9 8.8 24088
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.77 99.9 0.281 8.9
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 THROUGHOUT 5ev6 1.68 49.386 24038 1187 99.59 0.16 0.1577 0.1724 0.208 0.2207 25.78
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] -0.257 1.241 -0.984
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.428 r_dihedral_angle_4_deg 20.678 r_dihedral_angle_3_deg 14.929 r_dihedral_angle_1_deg 7.739 r_lrange_other 7.268 r_lrange_it 7.265 r_dihedral_angle_other_3_deg 6.705 r_scangle_it 6.054 r_scangle_other 6.051 r_scbond_it 4.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.428 r_dihedral_angle_4_deg 20.678 r_dihedral_angle_3_deg 14.929 r_dihedral_angle_1_deg 7.739 r_lrange_other 7.268 r_lrange_it 7.265 r_dihedral_angle_other_3_deg 6.705 r_scangle_it 6.054 r_scangle_other 6.051 r_scbond_it 4.259 r_scbond_other 4.259 r_mcangle_it 3.569 r_mcangle_other 3.568 r_mcbond_it 2.639 r_mcbond_other 2.632 r_angle_refined_deg 1.528 r_angle_other_deg 1.338 r_symmetry_xyhbond_nbd_refined 0.255 r_nbd_other 0.227 r_nbd_refined 0.22 r_symmetry_nbd_other 0.199 r_symmetry_nbd_refined 0.188 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.168 r_symmetry_xyhbond_nbd_other 0.111 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.079 r_metal_ion_refined 0.044 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1728 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing