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Crystal structure of the mCD1d/xxq (JJ300)/iNKTCR ternary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IRS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 295 0.1 m sodium malonate pH 4.0, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.03 59.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.976 α = 90 b = 191.441 β = 90 c = 151.369 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 PILATUS3 6M 2017-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97 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 2.05 50 98 0.109 0.119 0.048 5.8 6 71307
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 2.05 2.12 93.5 0.614 0.691 0.309 0.736 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4IRS 2.05 41.54 67239 3613 98.13 0.1867 0.1849 0.1933 0.2192 0.2252 RANDOM 38.54
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] -0.28 2.19 -1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.719 r_dihedral_angle_4_deg 15.735 r_dihedral_angle_3_deg 12.845 r_dihedral_angle_1_deg 6.866 r_angle_refined_deg 1.088 r_angle_other_deg 0.805 r_chiral_restr 0.051 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.719 r_dihedral_angle_4_deg 15.735 r_dihedral_angle_3_deg 12.845 r_dihedral_angle_1_deg 6.866 r_angle_refined_deg 1.088 r_angle_other_deg 0.805 r_chiral_restr 0.051 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6338 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 178
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing