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Structure of alpha-GSA[16,6P] 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 4 295 12% PEG 3350, 0.1M sodium malonate pH 4.0
Crystal Properties Matthews coefficient Solvent content 3 59.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.891 α = 90 b = 190.13 β = 90 c = 151.043 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 2017-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.98 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 2.35 40 92.6 0.089 0.101 0.045 7.7 4.2 43262
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 2.35 2.43 93.7 0.449 0.51 0.231 0.792 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 2.36 40 41929 1332 91.74 0.1935 0.1922 0.1964 0.2351 0.2358 RANDOM 47.189
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] -0.29 0.84 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.528 r_dihedral_angle_4_deg 14.387 r_dihedral_angle_3_deg 13.729 r_dihedral_angle_1_deg 6.34 r_angle_refined_deg 1.275 r_angle_other_deg 1.005 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_bond_other_d 0.004 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.528 r_dihedral_angle_4_deg 14.387 r_dihedral_angle_3_deg 13.729 r_dihedral_angle_1_deg 6.34 r_angle_refined_deg 1.275 r_angle_other_deg 1.005 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6364 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 127
Software Software Software Name Purpose HKL-2000 data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction