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Crystal structure of MCD1D/INKTCR TERNARY COMPLEX bound to glycolipid (XXW)
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 295 0.1 m sodium malonate pH 4.0, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.01 59.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.948 α = 90 b = 190.723 β = 90 c = 151.145 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 2017-11-05 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 50 99.6 0.088 0.095 0.037 5.5 6.5 77265
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 2.07 99.4 0.663 0.731 0.301 0.759 5.6
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 4IRS 2 47.1 73109 3839 99.62 0.1861 0.1846 0.2143 0.2053 RANDOM 32.023
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 0.73 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.749 r_dihedral_angle_4_deg 16.115 r_dihedral_angle_3_deg 12.402 r_dihedral_angle_1_deg 6.646 r_angle_refined_deg 0.936 r_angle_other_deg 0.744 r_chiral_restr 0.045 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.749 r_dihedral_angle_4_deg 16.115 r_dihedral_angle_3_deg 12.402 r_dihedral_angle_1_deg 6.646 r_angle_refined_deg 0.936 r_angle_other_deg 0.744 r_chiral_restr 0.045 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6392 Nucleic Acid Atoms Solvent Atoms 685 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing