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Structure of T-cell immunoreceptor with immunoglobulin and ITIM domains (TIGIT)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IKF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 1.3M Ammonium Sulfate, 0.1M MES pH 6.0, Vapor diffusion, Sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.54 51.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.951 α = 90 b = 74.671 β = 92.39 c = 43.346 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 CCD ADSC QUANTUM 315 2010-07-15 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9793 NSLS X29A
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 1.7 50 99.7 0.038 16.4 7.3 27916 14.1
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 1.7 1.73 100 0.535 7.1 1413
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MIR THROUGHOUT 1IKF 1.7 43.31 27504 1376 98.22 0.2087 0.2072 0.237 0.2571 RANDOM 18.6664
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] 0.15 0.21 -0.09 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.235 r_dihedral_angle_4_deg 15.852 r_dihedral_angle_3_deg 15.661 r_dihedral_angle_1_deg 7.027 r_scangle_it 4.412 r_scbond_it 2.799 r_mcangle_it 1.782 r_angle_refined_deg 1.678 r_mcbond_it 0.939 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.235 r_dihedral_angle_4_deg 15.852 r_dihedral_angle_3_deg 15.661 r_dihedral_angle_1_deg 7.027 r_scangle_it 4.412 r_scbond_it 2.799 r_mcangle_it 1.782 r_angle_refined_deg 1.678 r_mcbond_it 0.939 r_chiral_restr 0.116 r_bond_refined_d 0.015 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1648 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction PHASER phasing