☰ Navigation Tabs
Crystal structure of the mCD1d/xxp (JJ295) /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 295 0.1 m sodium malonate pH 4.0, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.03 59.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.967 α = 90 b = 191.858 β = 90.02 c = 150.957 γ = 90
Symmetry Space Group C 1 2 1
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 3 50 96.4 0.127 0.147 0.072 5.6 3.7 42754
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 3 3.11 90.9 0.335 0.394 0.203 0.866 3.3
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 3 49.75 40603 2142 95.17 0.2175 0.2154 0.2181 0.2578 0.2593 RANDOM 52.394
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] 0.52 -0.73 3.38 -3.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.923 r_dihedral_angle_3_deg 12.002 r_dihedral_angle_4_deg 10.044 r_dihedral_angle_1_deg 4.844 r_angle_refined_deg 0.711 r_angle_other_deg 0.635 r_chiral_restr 0.029 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.923 r_dihedral_angle_3_deg 12.002 r_dihedral_angle_4_deg 10.044 r_dihedral_angle_1_deg 4.844 r_angle_refined_deg 0.711 r_angle_other_deg 0.635 r_chiral_restr 0.029 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12766 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 370
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing