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Crystal Structure of Bel-1 Extended Spectrum Beta-lactamase in Hexagonal Form
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 7.5 293 0.2M Magnesium chloride hexahydrate, 0.1M HEPES sodium pH 7.5, 30% v/v 2-Propanol
Crystal Properties Matthews coefficient Solvent content 2.63 53.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.192 α = 90 b = 121.192 β = 90 c = 72.128 γ = 120
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 X ray optics 2022-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.5 29.126 99.9 0.99 18.4 7.6 96340
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 1.5 8.22 0.418
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 1.5 29.126 96119 4975 99.751 0.153 0.15 0.1499 0.2088 0.2087 20.523
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] -0.048 -0.024 -0.048 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.773 r_dihedral_angle_3_deg 13.635 r_dihedral_angle_2_deg 9.008 r_dihedral_angle_1_deg 6.103 r_rigid_bond_restr 5.93 r_lrange_it 4.403 r_lrange_other 4.398 r_scangle_it 3.476 r_scangle_other 3.476 r_scbond_it 2.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.773 r_dihedral_angle_3_deg 13.635 r_dihedral_angle_2_deg 9.008 r_dihedral_angle_1_deg 6.103 r_rigid_bond_restr 5.93 r_lrange_it 4.403 r_lrange_other 4.398 r_scangle_it 3.476 r_scangle_other 3.476 r_scbond_it 2.702 r_scbond_other 2.702 r_mcangle_other 2.532 r_mcangle_it 2.526 r_mcbond_it 2.018 r_angle_refined_deg 2.009 r_mcbond_other 2.003 r_angle_other_deg 0.675 r_metal_ion_refined 0.454 r_symmetry_xyhbond_nbd_refined 0.275 r_symmetry_nbd_refined 0.255 r_nbd_refined 0.239 r_xyhbond_nbd_refined 0.227 r_nbd_other 0.209 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.183 r_chiral_restr 0.104 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.053 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4063 Nucleic Acid Atoms Solvent Atoms 608 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing