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Crystal structure of human CD160 and HVEM complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FHQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M HEPES pH7.0, 30% (V/V) Jeffamine ED-2001 pH7.0, and 0.1 M sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 2.9 57.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.93 α = 90 b = 87.93 β = 90 c = 157.698 γ = 90
Symmetry Space Group I 41 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 315 2016-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 2.88 50 99.9 0.178 14.5 14.1 7332
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 2.88 2.93 1.552
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 4FHQ 2.88 20 6939 344 99.45 0.23614 0.23415 0.27363 0.2769 RANDOM 71.963
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] 3.03 3.03 -6.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.667 r_dihedral_angle_4_deg 24.399 r_dihedral_angle_3_deg 20.246 r_long_range_B_refined 11.958 r_long_range_B_other 11.954 r_scangle_other 8.103 r_mcangle_other 8.065 r_mcangle_it 8.063 r_dihedral_angle_1_deg 7.407 r_scbond_it 5.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.667 r_dihedral_angle_4_deg 24.399 r_dihedral_angle_3_deg 20.246 r_long_range_B_refined 11.958 r_long_range_B_other 11.954 r_scangle_other 8.103 r_mcangle_other 8.065 r_mcangle_it 8.063 r_dihedral_angle_1_deg 7.407 r_scbond_it 5.416 r_scbond_other 5.413 r_mcbond_it 5.082 r_mcbond_other 5.053 r_angle_refined_deg 1.913 r_angle_other_deg 1.028 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1537 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing