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Crystal structure of the mCD1d/EF77/iNKTCR ternary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q7Y 2Q7Y and 3QUZ experimental model PDB 3QUZ 2Q7Y and 3QUZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295.5 20% PEG 4000, 0.2M ammonium citrate dibasic
Crystal Properties Matthews coefficient Solvent content 3.13 60.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.96 α = 90 b = 191.07 β = 90 c = 151.08 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 2014-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9767 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.9 95.695 97.4 0.172 0.206 0.111 5.9 3.2 25092 32.27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 99.1 0.594 0.594 0.384 1.2 3.4 3686
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 2Q7Y and 3QUZ 2.9 95.54 23746 1272 97.07 0.21 0.2069 0.211 0.2672 0.2655 RANDOM 37.567
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] -0.07 -0.11 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.363 r_dihedral_angle_4_deg 18.914 r_dihedral_angle_3_deg 15.951 r_dihedral_angle_1_deg 6.898 r_mcangle_it 1.558 r_angle_refined_deg 1.466 r_angle_other_deg 0.968 r_mcbond_it 0.86 r_mcbond_other 0.86 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.363 r_dihedral_angle_4_deg 18.914 r_dihedral_angle_3_deg 15.951 r_dihedral_angle_1_deg 6.898 r_mcangle_it 1.558 r_angle_refined_deg 1.466 r_angle_other_deg 0.968 r_mcbond_it 0.86 r_mcbond_other 0.86 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6165 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 122
Software Software Software Name Purpose Blu-Ice data collection MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction