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Crystal structure of GEM42 TCR-CD1b-GMM complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L2J 5L2J, 4G8F experimental model PDB 4G8F 5L2J, 4G8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 1.5-2M NH4SO4, 0.1M Tris-HCl pH8.5, 10mM MgCl2, 10mM CeCl2
Crystal Properties Matthews coefficient Solvent content 4.09 69.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.998 α = 90 b = 174.998 β = 90 c = 170.869 γ = 120
Symmetry Space Group P 64 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2015-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.2 47.73 78.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.37 100 7.76 0.082 0.083 0.011 0.638 61.1 3727
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 5L2J, 4G8F 3.2 47.73 26029 1259 99.97 0.219 0.218 0.2392 0.2274 RANDOM 80.56
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] -2.7014 -2.7014 5.4028
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.08 t_omega_torsion 2.04 t_angle_deg 0.92 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.08 t_omega_torsion 2.04 t_angle_deg 0.92 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6341 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 150
Software Software Software Name Purpose BUSTER refinement SCALA data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction