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Broadly neutralizing DARPin bnD.3 in complex with the HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other in house model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277.15 0.2M Ca Acetate, 0.1 Na Acetate pH 5.5, 30% PEG 2K MME
Crystal Properties Matthews coefficient Solvent content 2.08 40.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.4 α = 90 b = 67.06 β = 90 c = 93.11 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 PIXEL DECTRIS PILATUS 2M 2016-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00004 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.9 54.42 99.6 0.105 0.121 0.996 8.09 3.944 47910 32.086
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 0.682
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 in house model 1.9 46.6 24254 1279 99.91 0.18316 0.18077 0.1888 0.22732 0.2323 RANDOM 31.731
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] 2.22 -0.48 -1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.694 r_dihedral_angle_3_deg 15.582 r_dihedral_angle_4_deg 6.514 r_long_range_B_refined 6.433 r_long_range_B_other 6.432 r_dihedral_angle_1_deg 6.138 r_scangle_other 2.371 r_angle_refined_deg 1.787 r_mcangle_it 1.606 r_mcangle_other 1.606
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.694 r_dihedral_angle_3_deg 15.582 r_dihedral_angle_4_deg 6.514 r_long_range_B_refined 6.433 r_long_range_B_other 6.432 r_dihedral_angle_1_deg 6.138 r_scangle_other 2.371 r_angle_refined_deg 1.787 r_mcangle_it 1.606 r_mcangle_other 1.606 r_scbond_it 1.495 r_scbond_other 1.495 r_angle_other_deg 1.489 r_mcbond_other 1.047 r_mcbond_it 1.046 r_chiral_restr 0.092 r_bond_refined_d 0.014 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 2622 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction