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The crystal structure of human VISTA extra cellular domain in complex with Fab fragment of pH-selective anti-VISTA antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OIL experimental model PDB 6MVL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1 M BIS-TRIS propane, 0.2 M NaBr, 22%PEG3350
Crystal Properties Matthews coefficient Solvent content 2.63 53.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 207.659 α = 90 b = 39.512 β = 117.121 c = 177.979 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 EIGER2 X 16M 2022-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9998 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.593 158.409 84.6 0.996 8.9 4.27 26185
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 2.593 2.837 52.7 0.695 4.58
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.593 158.409 26185 1291 63.9 0.239 0.2366 0.2406 0.291 0.2924 51.929
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] 0.294 -0.481 -0.97 0.766
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.999 r_dihedral_angle_3_deg 12.86 r_dihedral_angle_1_deg 7.227 r_lrange_it 5.205 r_lrange_other 5.202 r_dihedral_angle_2_deg 3.639 r_mcangle_it 3.35 r_mcangle_other 3.35 r_scangle_it 2.401 r_scangle_other 2.401
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.999 r_dihedral_angle_3_deg 12.86 r_dihedral_angle_1_deg 7.227 r_lrange_it 5.205 r_lrange_other 5.202 r_dihedral_angle_2_deg 3.639 r_mcangle_it 3.35 r_mcangle_other 3.35 r_scangle_it 2.401 r_scangle_other 2.401 r_mcbond_it 1.9 r_mcbond_other 1.9 r_scbond_it 1.332 r_scbond_other 1.332 r_angle_refined_deg 0.941 r_angle_other_deg 0.577 r_nbtor_refined 0.158 r_symmetry_nbd_other 0.155 r_nbd_refined 0.145 r_xyhbond_nbd_refined 0.107 r_nbd_other 0.107 r_symmetry_xyhbond_nbd_refined 0.088 r_symmetry_nbtor_other 0.075 r_symmetry_nbd_refined 0.074 r_ncsr_local_group_3 0.061 r_ncsr_local_group_1 0.045 r_chiral_restr 0.044 r_ncsr_local_group_2 0.041 r_bond_other_d 0.026 r_symmetry_xyhbond_nbd_other 0.019 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8440 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing