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Crystal structure of the metallo-beta-lactamase Sfh-I in complex with the bisthiazolidine inhibitor L-CS319
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SD9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M sodium acetate, 27% w/v PEG 3350, pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.95 36.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.77 α = 90 b = 86.7 β = 90.09 c = 72.23 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 6M-F 2015-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
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 1.3 19.42 97.6 0.118 7.6 5.8 91618
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 1.3 1.32 95.5 0.521 4.2 9.9
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 (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 3SD9 1.3 19.42 91618 4742 96.98 0.16159 0.16018 0.1639 0.18863 0.1922 RANDOM 11.754
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] -0.7 -0.45 -1.95 2.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.673 r_dihedral_angle_4_deg 19.929 r_dihedral_angle_3_deg 12.481 r_dihedral_angle_1_deg 6.236 r_long_range_B_refined 5.624 r_long_range_B_other 5.322 r_scangle_other 2.883 r_scbond_it 1.97 r_scbond_other 1.966 r_mcangle_it 1.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.673 r_dihedral_angle_4_deg 19.929 r_dihedral_angle_3_deg 12.481 r_dihedral_angle_1_deg 6.236 r_long_range_B_refined 5.624 r_long_range_B_other 5.322 r_scangle_other 2.883 r_scbond_it 1.97 r_scbond_other 1.966 r_mcangle_it 1.713 r_mcangle_other 1.712 r_angle_refined_deg 1.569 r_angle_other_deg 1.441 r_mcbond_it 1.14 r_mcbond_other 1.14 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3622 Nucleic Acid Atoms Solvent Atoms 603 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing