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Crystal structure of LukGH from Staphylococcus aureus in complex with a neutralising antibody
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.2 293 Drop contained 200 nl Fab-LukGH at 1:1 ratio + 50 nl seed stock + 150 nl reservoir solution [0.3 M NaCl, 26% polyethylene glycol (PEG) 8000, 0.1 M phosphate citrate pH 4.2]. The seed solution was obtained from 40 % PEG 300, 0.1 M phosphate-citrate pH 4.2, 0.3 M NaCl, 20 mM HEPES pH 7.5.
Crystal Properties Matthews coefficient Solvent content 2.96 58.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.79 α = 90 b = 160.932 β = 101.18 c = 119.484 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 CCD MARMOSAIC 225 mm CCD focusing mirrors 2014-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.0000 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.84 48.8 99.3 0.108 0.993 10.1 3.7 64655
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 2.84 2.91 92.5 0.883 1.4 3.5
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 MOLECULAR REPLACEMENT THROUGHOUT 2.84 48.54 61207 3277 99.08 0.19888 0.19681 0.2008 0.23727 0.2356 RANDOM 73.8
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] 1.84 2.68 -5.01 1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.006 r_dihedral_angle_3_deg 19.678 r_dihedral_angle_4_deg 17.018 r_dihedral_angle_1_deg 7.829 r_long_range_B_refined 5.939 r_long_range_B_other 5.939 r_scangle_other 4.035 r_mcangle_it 3.607 r_mcangle_other 3.607 r_scbond_it 2.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.006 r_dihedral_angle_3_deg 19.678 r_dihedral_angle_4_deg 17.018 r_dihedral_angle_1_deg 7.829 r_long_range_B_refined 5.939 r_long_range_B_other 5.939 r_scangle_other 4.035 r_mcangle_it 3.607 r_mcangle_other 3.607 r_scbond_it 2.446 r_scbond_other 2.445 r_mcbond_it 2.197 r_mcbond_other 2.197 r_angle_refined_deg 1.488 r_angle_other_deg 0.843 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 15744 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing