☰ Navigation Tabs
Crystal structure of the RV144 C1-C2 specific antibody CH54 Fab in complex with HIV-1 CLADE A/E GP120 and M48U1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 294 25% PEG 4000
0.1 M MES pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.17 43.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.827 α = 90 b = 42.231 β = 115.24 c = 119.754 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 2018-03-25 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) 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 95.9 0.174 11.1 3.2 16963
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 2.9 2.95 97.3 0.833 1 3.1
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 4RFO 2.91 39.68 16155 807 94.5 0.252 0.25 0.2499 0.307 0.3063 RANDOM 89.89
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] 0.85 -0.23 -1.94 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.71 r_dihedral_angle_4_deg 23.253 r_dihedral_angle_3_deg 21.208 r_long_range_B_refined 10.321 r_long_range_B_other 10.321 r_dihedral_angle_1_deg 7.639 r_scangle_other 4.796 r_mcangle_it 4.012 r_mcangle_other 4.012 r_scbond_it 2.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.71 r_dihedral_angle_4_deg 23.253 r_dihedral_angle_3_deg 21.208 r_long_range_B_refined 10.321 r_long_range_B_other 10.321 r_dihedral_angle_1_deg 7.639 r_scangle_other 4.796 r_mcangle_it 4.012 r_mcangle_other 4.012 r_scbond_it 2.818 r_scbond_other 2.818 r_mcbond_it 2.447 r_mcbond_other 2.447 r_angle_refined_deg 1.651 r_angle_other_deg 1.379 r_chiral_restr 0.067 r_bond_refined_d 0.008 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 6027 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing