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Crystal structure of OXA-517 beta-lactamase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4S2P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M MES pH 6.5 and 20% (w/v) PEG10000
Crystal Properties Matthews coefficient Solvent content 2.22 44.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.8 α = 90 b = 125.046 β = 94.65 c = 82.656 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 EIGER X 9M 2016-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980104506016 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.86 46.18 99.6 0.16 0.99 6.8 3.7 84548 -3 24.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.97 99.2 1.25 0.35 1 3
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 4s2p 1.86 46.18 80268 4277 99.65 0.17246 0.17003 0.1811 0.21885 0.2268 RANDOM 39.753
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] 0.5 0.01 -0.95 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.434 r_dihedral_angle_4_deg 17.96 r_dihedral_angle_3_deg 13.328 r_long_range_B_refined 8.293 r_long_range_B_other 8.293 r_scangle_other 7.134 r_dihedral_angle_1_deg 5.797 r_scbond_it 5.279 r_scbond_other 5.277 r_mcangle_it 4.742
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.434 r_dihedral_angle_4_deg 17.96 r_dihedral_angle_3_deg 13.328 r_long_range_B_refined 8.293 r_long_range_B_other 8.293 r_scangle_other 7.134 r_dihedral_angle_1_deg 5.797 r_scbond_it 5.279 r_scbond_other 5.277 r_mcangle_it 4.742 r_mcangle_other 4.741 r_mcbond_it 3.809 r_mcbond_other 3.807 r_angle_refined_deg 1.367 r_angle_other_deg 0.961 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 7952 Nucleic Acid Atoms Solvent Atoms 735 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing