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Crystal structure of broad neutralizing antibody 10E8 with long epitope bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G6F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 2.5 mM DPC
50% MPD
200 mM phosphate
100 mM TRIS
Crystal Properties Matthews coefficient Solvent content 3.24 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.633 α = 90 b = 81.231 β = 90 c = 254.216 γ = 90
Symmetry Space Group I 2 2 2
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 ADSC QUANTUM 270 2016-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 2.4 52.4 90 0.046 0.971 34 9.7 24652
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 2.4 2.49 56.2 0.202 8 7
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 4g6f 2.4 52.4 23462 1187 89.39 0.19366 0.19175 0.1966 0.23041 0.2327 RANDOM 40.341
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] 1.07 1.6 -2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.448 r_dihedral_angle_4_deg 18.346 r_dihedral_angle_3_deg 16.007 r_dihedral_angle_1_deg 7.052 r_long_range_B_refined 5.372 r_long_range_B_other 5.294 r_mcangle_it 1.997 r_mcangle_other 1.997 r_scangle_other 1.78 r_angle_refined_deg 1.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.448 r_dihedral_angle_4_deg 18.346 r_dihedral_angle_3_deg 16.007 r_dihedral_angle_1_deg 7.052 r_long_range_B_refined 5.372 r_long_range_B_other 5.294 r_mcangle_it 1.997 r_mcangle_other 1.997 r_scangle_other 1.78 r_angle_refined_deg 1.431 r_scbond_it 1.31 r_mcbond_it 1.125 r_mcbond_other 1.124 r_scbond_other 1.026 r_angle_other_deg 0.763 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 3558 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing