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Human antibody 32D6 Fab in complex with H1N1 influenza A virus HA1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GBN 3GBN, 3N9G experimental model PDB 3N9G 3GBN, 3N9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 14%(w/v) PEG 8000, 160mM Calcium acetate, 20%(v/v) glycerol, 80mM Sodium Cacodylate, Hydrochloric acid
Crystal Properties Matthews coefficient Solvent content 3.94 68.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.743 α = 90 b = 181.743 β = 90 c = 248.091 γ = 120
Symmetry Space Group P 31 1 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 RAYONIX MX300-HS 2017-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1.0000 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.15 20 98.6 0.077 14.7 3.2 79824
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 3.15 3.26 99.3 0.554 2.1 3.2
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 3GBN, 3N9G 3.15 20 72829 3824 94.55 0.17792 0.17511 0.1785 0.23287 0.2348 RANDOM 82.545
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] 0.17 0.08 0.17 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.965 r_dihedral_angle_3_deg 17.646 r_dihedral_angle_4_deg 16.043 r_long_range_B_other 11.424 r_long_range_B_refined 11.422 r_mcangle_it 8.079 r_mcangle_other 8.078 r_dihedral_angle_1_deg 8.036 r_scangle_other 7.547 r_mcbond_it 4.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.965 r_dihedral_angle_3_deg 17.646 r_dihedral_angle_4_deg 16.043 r_long_range_B_other 11.424 r_long_range_B_refined 11.422 r_mcangle_it 8.079 r_mcangle_other 8.078 r_dihedral_angle_1_deg 8.036 r_scangle_other 7.547 r_mcbond_it 4.908 r_mcbond_other 4.905 r_scbond_it 4.472 r_scbond_other 4.472 r_angle_refined_deg 1.532 r_angle_other_deg 0.972 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 20354 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing