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Structure of alpha-GC[8,18] bound by CD1d and in complex with the Va14Vb8.2 TCR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q7Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 295 8% Tacsimate pH 4.0
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.73 54.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.641 α = 90 b = 190.354 β = 90 c = 150.785 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 315r 2015-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.979 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.85 40 99.8 0.139 0.159 0.075 5.9 4.5 26851
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.9 100 0.559 0.638 0.301 0.704 4.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2Q7Y 2.85 39.32 25731 1095 99.67 0.2102 0.2085 0.2504 0.2186 RANDOM 39.953
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] 0.08 -0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.055 r_dihedral_angle_4_deg 16.071 r_dihedral_angle_3_deg 14.468 r_dihedral_angle_1_deg 6.849 r_angle_refined_deg 1.276 r_angle_other_deg 1.029 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.055 r_dihedral_angle_4_deg 16.071 r_dihedral_angle_3_deg 14.468 r_dihedral_angle_1_deg 6.849 r_angle_refined_deg 1.276 r_angle_other_deg 1.029 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6367 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 126
Software Software Software Name Purpose HKL-2000 data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction