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Crystal structure of the complex between OX40L and 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 6.5 293 8% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.44 72.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.903 α = 90 b = 111.903 β = 90 c = 233.238 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 2003-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.9999 ALS 5.0.2
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 2.4 50 99.9 0.055 11.8 6.1 22255 -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 2.4 2.49 100 0.505 2.3 6.1 2195
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 2.41 30 -3 22103 2221 99.86 0.21248 0.21248 0.20825 0.2104 0.2511 0.2463 RANDOM 38.975
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] 1.91 0.96 1.91 -2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.79 r_dihedral_angle_3_deg 14.019 r_dihedral_angle_4_deg 13.332 r_dihedral_angle_1_deg 5.866 r_mcangle_it 2.877 r_scangle_it 2.852 r_mcbond_it 2.242 r_scbond_it 1.909 r_angle_refined_deg 1.109 r_angle_other_deg 0.694
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.79 r_dihedral_angle_3_deg 14.019 r_dihedral_angle_4_deg 13.332 r_dihedral_angle_1_deg 5.866 r_mcangle_it 2.877 r_scangle_it 2.852 r_mcbond_it 2.242 r_scbond_it 1.909 r_angle_refined_deg 1.109 r_angle_other_deg 0.694 r_mcbond_other 0.368 r_symmetry_hbond_refined 0.328 r_nbd_refined 0.172 r_nbtor_refined 0.17 r_nbd_other 0.168 r_symmetry_vdw_other 0.158 r_xyhbond_nbd_refined 0.155 r_symmetry_vdw_refined 0.124 r_nbtor_other 0.08 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 2067 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement AMoRE phasing