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Crystal structure of broadly neutralizing anti-HIV-1 antibody 4E10, mutant Npro, with peptide bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WY7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 291.15 100mM sodium acetate; 34% PEG4000; 225mM ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.75 55.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.509 α = 90 b = 44.5 β = 113.7 c = 85.13 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M-F 2016-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979133 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 1.49 22.25 99.5 0.081 0.035 0.998 11.9 6 88101
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.49 1.57 99.5 0.77 0.344 0.666 2.4 5.8
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 4WY7 1.49 22.25 85514 2579 99.38 0.12977 0.12857 0.1281 0.1687 0.1685 RANDOM 19.179
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] -0.52 -0.28 0.09 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.721 r_sphericity_free 22.282 r_dihedral_angle_4_deg 16.518 r_dihedral_angle_3_deg 11.152 r_sphericity_bonded 8.992 r_dihedral_angle_1_deg 6.532 r_rigid_bond_restr 5.475 r_long_range_B_refined 3.996 r_long_range_B_other 3.741 r_scangle_other 3.661
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.721 r_sphericity_free 22.282 r_dihedral_angle_4_deg 16.518 r_dihedral_angle_3_deg 11.152 r_sphericity_bonded 8.992 r_dihedral_angle_1_deg 6.532 r_rigid_bond_restr 5.475 r_long_range_B_refined 3.996 r_long_range_B_other 3.741 r_scangle_other 3.661 r_scbond_other 3.293 r_scbond_it 3.291 r_mcangle_other 2.492 r_mcangle_it 2.486 r_mcbond_it 2.159 r_mcbond_other 2.149 r_angle_refined_deg 1.617 r_angle_other_deg 0.798 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3369 Nucleic Acid Atoms Solvent Atoms 481 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing