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Crystal structure of murine OX40L bound to human OX40
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HEW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 0.1 M NaCl, 1.4 M Ammonium Sulfate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.84 67.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.729 α = 90 b = 104.729 β = 90 c = 478.161 γ = 120
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 210 torroidal mirror 2003-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.9330 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 30 98.6 0.069 12.2 4.6 68124 68124 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 96.4 0.272 2.1 4.6 6549
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2 30 67693 60840 6853 98.82 0.2232 0.2232 0.22054 0.2243 0.24713 0.2517 RANDOM 34.815
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] 1.1 0.55 1.1 -1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.94 r_dihedral_angle_4_deg 14.82 r_dihedral_angle_3_deg 13.371 r_dihedral_angle_1_deg 5.786 r_scangle_it 3.346 r_mcangle_it 3.073 r_mcbond_it 2.469 r_scbond_it 2.335 r_angle_refined_deg 1.041 r_angle_other_deg 0.692
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.94 r_dihedral_angle_4_deg 14.82 r_dihedral_angle_3_deg 13.371 r_dihedral_angle_1_deg 5.786 r_scangle_it 3.346 r_mcangle_it 3.073 r_mcbond_it 2.469 r_scbond_it 2.335 r_angle_refined_deg 1.041 r_angle_other_deg 0.692 r_mcbond_other 0.398 r_nbd_refined 0.189 r_nbd_other 0.173 r_symmetry_vdw_other 0.173 r_nbtor_refined 0.167 r_symmetry_hbond_refined 0.12 r_xyhbond_nbd_refined 0.118 r_symmetry_vdw_refined 0.11 r_nbtor_other 0.078 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4175 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement AMoRE phasing