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OXA-48 in complex with FPI-1465
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.005 M CoCl2, 0.005 M CdCl2, 0.005 M MgCl2, 0.005 M NiCl2, 0.1 M HEPES pH 7.5, 12% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.65 53.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.76 α = 90 b = 75.47 β = 90 c = 106.97 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 CCD RAYONIX MX-300 2015-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.00 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.96 43.64 99.7 22.6 7.3 42805 16.67
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 3HBR 1.96 43.64 40619 2124 99.7 0.17 0.168 0.1804 0.21 0.2214 RANDOM 25.4
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] -1.2 1.21 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.418 r_dihedral_angle_4_deg 20.202 r_dihedral_angle_3_deg 12.944 r_long_range_B_refined 5.918 r_dihedral_angle_1_deg 5.873 r_long_range_B_other 5.716 r_scangle_other 4.546 r_scbond_it 3.08 r_scbond_other 3.079 r_mcangle_it 2.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.418 r_dihedral_angle_4_deg 20.202 r_dihedral_angle_3_deg 12.944 r_long_range_B_refined 5.918 r_dihedral_angle_1_deg 5.873 r_long_range_B_other 5.716 r_scangle_other 4.546 r_scbond_it 3.08 r_scbond_other 3.079 r_mcangle_it 2.586 r_mcangle_other 2.586 r_mcbond_it 1.95 r_mcbond_other 1.949 r_angle_refined_deg 1.78 r_angle_other_deg 0.889 r_chiral_restr 0.183 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.001 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 3942 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing