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Structure of antibody BA8 in complex with sulfated peptide from CCR5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XV1 experimental model PDB 6LDX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 10% PEG 1000,
10% PEG 8,000
Crystal Properties Matthews coefficient Solvent content 2.26 45.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.129 α = 90 b = 70.943 β = 97.93 c = 60.984 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 PILATUS3 S 6M 2021-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.75 40.68 98.7 0.128 0.052 0.997 11.7 6.8 42109
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 1.75 1.78 97.8 0.976 0.406 0.715 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.75 40.68 40803 1286 98.49 0.16666 0.16543 0.1749 0.2056 0.2106 RANDOM 16.631
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] -0.78 0.06 1.64 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.287 r_dihedral_angle_3_deg 11.36 r_dihedral_angle_1_deg 7.12 r_long_range_B_refined 5.026 r_long_range_B_other 4.904 r_scangle_other 3.65 r_mcangle_it 2.56 r_mcangle_other 2.559 r_scbond_it 2.351 r_scbond_other 2.351
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.287 r_dihedral_angle_3_deg 11.36 r_dihedral_angle_1_deg 7.12 r_long_range_B_refined 5.026 r_long_range_B_other 4.904 r_scangle_other 3.65 r_mcangle_it 2.56 r_mcangle_other 2.559 r_scbond_it 2.351 r_scbond_other 2.351 r_mcbond_it 1.617 r_mcbond_other 1.616 r_angle_refined_deg 1.58 r_angle_other_deg 0.569 r_chiral_restr 0.079 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3323 Nucleic Acid Atoms Solvent Atoms 433 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing