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Novel non-antibody protein scaffold targeting CD40L
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ALY PDB entries 1ALY & 1TEN experimental model PDB 1TEN PDB entries 1ALY & 1TEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 40% v/v PEG600, 0.1 M sodium acetate, 0.2 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 3.33 63.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.528 α = 90 b = 93.528 β = 90 c = 66.685 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 100 CCD RAYONIX MX225HE 2010-12-15 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) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.82 51.48 99.9 0.195 0.195 0.208 0.073 8.1 7.9 8406 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.82 2.83 0.796 0.349
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entries 1ALY & 1TEN 2.82 51.48 7531 829 99.59 0.22988 0.22515 0.2315 0.27321 0.2933 RANDOM 74.941
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] 26.53 26.53 -53.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.585 r_dihedral_angle_3_deg 15.407 r_dihedral_angle_4_deg 9.995 r_dihedral_angle_1_deg 7.346 r_long_range_B_refined 2.372 r_long_range_B_other 2.359 r_angle_refined_deg 1.271 r_mcangle_it 1.271 r_mcangle_other 1.27 r_scangle_other 1.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.585 r_dihedral_angle_3_deg 15.407 r_dihedral_angle_4_deg 9.995 r_dihedral_angle_1_deg 7.346 r_long_range_B_refined 2.372 r_long_range_B_other 2.359 r_angle_refined_deg 1.271 r_mcangle_it 1.271 r_mcangle_other 1.27 r_scangle_other 1.193 r_angle_other_deg 0.824 r_mcbond_other 0.728 r_mcbond_it 0.727 r_scbond_it 0.674 r_scbond_other 0.674 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1779 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing