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Crystal structure of human4-1BB ligand ectodomain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M SODIUM CHLORIDE, 0.1M BIS-TRIS PH6.5, 1.5M AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 4.03 69.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.846 α = 90 b = 121.846 β = 90 c = 33.575 γ = 120
Symmetry Space Group P 3 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 97 CCD ADSC CCD 2007-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A PAL/PLS 4A
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 2.3 50 100 0.08 100 13136 32
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 2.3 50 100 0.08 32 18.7
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 SAD THROUGHOUT NONE 2.3 39.88 12250 637 99.85 0.21976 0.21896 0.2169 0.23456 0.2362 RANDOM 24.787
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 36.442 r_dihedral_angle_4_deg 16.788 r_dihedral_angle_3_deg 15.244 r_dihedral_angle_1_deg 7.317 r_scangle_it 6.652 r_scbond_it 4.318 r_mcangle_it 2.334 r_angle_refined_deg 1.905 r_mcbond_it 1.272 r_chiral_restr 0.167
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.442 r_dihedral_angle_4_deg 16.788 r_dihedral_angle_3_deg 15.244 r_dihedral_angle_1_deg 7.317 r_scangle_it 6.652 r_scbond_it 4.318 r_mcangle_it 2.334 r_angle_refined_deg 1.905 r_mcbond_it 1.272 r_chiral_restr 0.167 r_bond_refined_d 0.027 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1176 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling