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Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-sulfatide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SCM PDB ENTRY 3SCM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.2 0.2M SODIUM CITRATE PH 6.2, 15% PEG 6000
Crystal Properties Matthews coefficient Solvent content 3.42 64.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.11 α = 90 b = 95.11 β = 90 c = 291.4 γ = 90
Symmetry Space Group P 41 21 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 2012-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 79.6 99.6 0.05 11.5 8.5 27729 2 95.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.16 98.1 0.43 2.3 7.5
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 PDB ENTRY 3SCM 3 36.49 27627 1391 99.56 0.1802 0.1775 0.1957 0.2316 0.2484 RANDOM 94.98
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] 1.4059 1.4059 -2.8117
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.43 t_omega_torsion 3.23 t_angle_deg 1.19 t_bond_d 0.01 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 3.43 t_omega_torsion 3.23 t_angle_deg 1.19 t_bond_d 0.01 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 6386 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 138
Software Software Software Name Purpose BUSTER refinement MOSFLM data reduction SCALA data scaling PHASER phasing