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The crystal structure of LIGHT in complex with HVEM and CD160
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RSU 4RSU, 6NG9 experimental model PDB 6NG9 4RSU, 6NG9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 291 0.2 M potassium iodide, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.09 60.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 214.689 α = 90 b = 214.689 β = 90 c = 214.689 γ = 90
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 MARMOSAIC 225 mm CCD 2016-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 3.5 34.83 99.9 0.195 0.2 0.044 0.999 16.1 20.7 20868
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 3.5 3.83 100 1.718 1.767 0.414 0.676 17.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4RSU, 6NG9 3.5 19.933 20765 1001 99.33 0.258 0.2566 0.2543 0.2847 0.2813 139.931
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.315 r_dihedral_angle_3_deg 16.113 r_dihedral_angle_4_deg 14.992 r_lrange_other 13.762 r_lrange_it 13.761 r_dihedral_angle_1_deg 7.187 r_mcangle_it 7.14 r_mcangle_other 7.14 r_scangle_it 5.843 r_scangle_other 5.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.315 r_dihedral_angle_3_deg 16.113 r_dihedral_angle_4_deg 14.992 r_lrange_other 13.762 r_lrange_it 13.761 r_dihedral_angle_1_deg 7.187 r_mcangle_it 7.14 r_mcangle_other 7.14 r_scangle_it 5.843 r_scangle_other 5.843 r_mcbond_it 4.082 r_mcbond_other 4.079 r_scbond_it 3.215 r_scbond_other 3.214 r_angle_other_deg 1.52 r_angle_refined_deg 1.29 r_symmetry_nbd_refined 0.386 r_nbd_other 0.349 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.193 r_nbd_refined 0.161 r_nbtor_refined 0.153 r_xyhbond_nbd_refined 0.134 r_symmetry_xyhbond_nbd_other 0.092 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.047 r_bond_other_d 0.012 r_gen_planes_other 0.006 r_bond_refined_d 0.005 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7929 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 201
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling MOLREP phasing