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Crystal structure of a representative of class A beta-lactamase from Bacteroides cellulosilyticus DSM 14838
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 291 0.4 M NaH2PO4/1.6 M K2HPO4
0.1 M Imidazole:HCl pH 8.0
0.2 M Sodium Chloride
Crystal Properties Matthews coefficient Solvent content 2.48 50.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.837 α = 90 b = 62.808 β = 90 c = 87.058 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 PIXEL DECTRIS PILATUS 6M 2016-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 1.07 40 98.9 0.062 35 6.5 133512
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.07 40 109930 5739 95.76 0.11573 0.11479 0.1209 0.134 0.1388 RANDOM 19.478
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] -0.18 0.42 -0.24
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.226 r_dihedral_angle_2_deg 35.862 r_dihedral_angle_1_deg 15.907 r_dihedral_angle_3_deg 12.092 r_sphericity_bonded 10.758 r_dihedral_angle_4_deg 6.218 r_rigid_bond_restr 6.188 r_long_range_B_refined 4.671 r_scangle_other 3.745 r_long_range_B_other 3.711
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.226 r_dihedral_angle_2_deg 35.862 r_dihedral_angle_1_deg 15.907 r_dihedral_angle_3_deg 12.092 r_sphericity_bonded 10.758 r_dihedral_angle_4_deg 6.218 r_rigid_bond_restr 6.188 r_long_range_B_refined 4.671 r_scangle_other 3.745 r_long_range_B_other 3.711 r_scbond_it 3.674 r_scbond_other 3.672 r_mcangle_other 2.021 r_mcangle_it 1.996 r_angle_refined_deg 1.851 r_mcbond_it 1.699 r_mcbond_other 1.62 r_angle_other_deg 1.293 r_chiral_restr 0.128 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_gen_planes_other 0.006 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2133 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling SHELXCD phasing