☰ Navigation Tabs
Rhesusized RV305 DH677.3 Fab bound to Clade A/E 93TH057 HIV-1 gp120 core.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MFP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 294 20% PEG 4000
0.1 M sodium citrate pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.39 48.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.182 α = 90 b = 82.664 β = 112.02 c = 111.899 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 PIXEL DECTRIS PILATUS 6M 2019-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 2.9 50 82.7 0.106 0.078 0.975 9.6 2.5 31091
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 2.9 2.95 86 0.627 0.467 0.714 1.1 2.5
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 6MFP 2.9 47.93 29478 1599 82.63 0.2572 0.25517 0.2547 0.29578 0.2897 RANDOM 63.955
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] 2.31 -1.3 -0.66 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.962 r_dihedral_angle_3_deg 27.357 r_dihedral_angle_4_deg 25.9 r_long_range_B_refined 10.792 r_long_range_B_other 10.792 r_scangle_other 6.239 r_mcangle_it 6.083 r_mcangle_other 6.083 r_dihedral_angle_1_deg 4.48 r_scbond_it 4.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.962 r_dihedral_angle_3_deg 27.357 r_dihedral_angle_4_deg 25.9 r_long_range_B_refined 10.792 r_long_range_B_other 10.792 r_scangle_other 6.239 r_mcangle_it 6.083 r_mcangle_other 6.083 r_dihedral_angle_1_deg 4.48 r_scbond_it 4.089 r_scbond_other 4.089 r_mcbond_it 3.816 r_mcbond_other 3.816 r_angle_refined_deg 1.72 r_angle_other_deg 1.523 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.004 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 11790 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 252
Software Software Software Name Purpose REFMAC refinement PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing