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Structure of the first-in-class checkpoint inhibitor Ipilimumab bound to human CTLA-4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I85
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 0.1M ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.99 58.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.844 α = 90 b = 197.502 β = 90 c = 148.117 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC QUANTUM 315 2009-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E
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 3 34.91 99.7 0.143 6.1 6.4 28514
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 3 3.05 99.9 0.82 6.6
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 1I85 3 34.91 26945 1447 99.21 0.2067 0.2035 0.2065 0.2677 0.2696 RANDOM 69.607
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] 3.82 -1.51 -2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.528 r_dihedral_angle_3_deg 19.574 r_dihedral_angle_4_deg 18.761 r_dihedral_angle_1_deg 6.899 r_angle_refined_deg 1.461 r_mcangle_it 1.104 r_scbond_it 0.61 r_mcbond_it 0.608 r_chiral_restr 0.091 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.528 r_dihedral_angle_3_deg 19.574 r_dihedral_angle_4_deg 18.761 r_dihedral_angle_1_deg 6.899 r_angle_refined_deg 1.461 r_mcangle_it 1.104 r_scbond_it 0.61 r_mcbond_it 0.608 r_chiral_restr 0.091 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8036 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing