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Structure of alpha-GSA[8,6P] 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 3QUZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 20% PEG 4000, 0.2M di-Ammonium tartrate
Crystal Properties Matthews coefficient Solvent content 2.97 58.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.18 α = 90 b = 190.168 β = 90 c = 150.965 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 PIXEL DECTRIS PILATUS 6M 2016-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979 SSRL BL9-2
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 2.2 40 99.4 0.083 0.094 0.043 8.8 4.4 57216
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 2.2 2.28 100 0.644 0.733 0.341 0.696 4.3
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 3QUZ 2.2 40 54364 2831 99.17 0.2057 0.2041 0.2082 0.2357 0.2387 RANDOM 41.42
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.261 r_dihedral_angle_3_deg 13.192 r_dihedral_angle_4_deg 13.023 r_dihedral_angle_1_deg 6.352 r_angle_refined_deg 1.324 r_angle_other_deg 0.938 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.261 r_dihedral_angle_3_deg 13.192 r_dihedral_angle_4_deg 13.023 r_dihedral_angle_1_deg 6.352 r_angle_refined_deg 1.324 r_angle_other_deg 0.938 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6339 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 144
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing