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Crystal structure of extended-spectrum beta-lactamase BEL-1 in complex with Imipenem
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EOE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 298 20% PEG4600, 20% MPD, 0.1M sodium citrate, pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.1 41.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.98 α = 90 b = 95.86 β = 91.97 c = 103.42 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 2013-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
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 1.79 51.68 93.2 0.084 7.5 2.4 91836 2 16.443
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 1.79 1.89 96.4 0.388 2.7 2.4
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 5EOE 1.79 51.68 87230 4579 92.72 0.16545 0.1635 0.1737 0.20239 0.2135 RANDOM 20.741
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.848 r_dihedral_angle_4_deg 19.37 r_dihedral_angle_3_deg 12.442 r_dihedral_angle_1_deg 6.11 r_long_range_B_refined 4.932 r_long_range_B_other 4.932 r_scangle_other 3.323 r_mcangle_it 2.319 r_mcangle_other 2.319 r_scbond_it 2.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.848 r_dihedral_angle_4_deg 19.37 r_dihedral_angle_3_deg 12.442 r_dihedral_angle_1_deg 6.11 r_long_range_B_refined 4.932 r_long_range_B_other 4.932 r_scangle_other 3.323 r_mcangle_it 2.319 r_mcangle_other 2.319 r_scbond_it 2.212 r_scbond_other 2.212 r_angle_refined_deg 1.767 r_mcbond_it 1.653 r_mcbond_other 1.652 r_angle_other_deg 0.961 r_chiral_restr 0.107 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.004 r_gen_planes_other 0.001 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 7862 Nucleic Acid Atoms Solvent Atoms 685 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement MOLREP model building SCALA data scaling iMOSFLM data reduction