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Complex of Human CD40 Ectodomain with Lob 7.4 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 NA 2 VAPOR DIFFUSION, HANGING DROP 293 NA
Crystal Properties Matthews coefficient Solvent content 2.27 45.86 2.27 45.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.753 α = 90 b = 158.753 β = 90 c = 93.622 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS PILATUS 6M-F 2015-04-04 M SINGLE WAVELENGTH 2 2 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2015-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976254 ESRF ID23-1 2 SYNCHROTRON ESRF BEAMLINE ID23-1 0.969995 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.99 52 99.9 0.161 0.998 13.7 13.7 27589
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.99 3.18 99.3 0.912 2.4 6.2
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 1U6A 2.99 137.48 26355 1319 99.67 0.18707 0.18482 0.1896 0.23121 0.2286 RANDOM 84.715
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] 2.59 1.3 2.59 -8.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.454 r_dihedral_angle_3_deg 20.7 r_dihedral_angle_4_deg 18.582 r_long_range_B_refined 14.058 r_long_range_B_other 14.057 r_scangle_other 11.561 r_dihedral_angle_1_deg 10.747 r_mcangle_it 10.217 r_mcangle_other 10.215 r_scbond_it 8.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.454 r_dihedral_angle_3_deg 20.7 r_dihedral_angle_4_deg 18.582 r_long_range_B_refined 14.058 r_long_range_B_other 14.057 r_scangle_other 11.561 r_dihedral_angle_1_deg 10.747 r_mcangle_it 10.217 r_mcangle_other 10.215 r_scbond_it 8.25 r_scbond_other 8.25 r_mcbond_it 7.148 r_mcbond_other 7.135 r_angle_refined_deg 2.134 r_angle_other_deg 1.154 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 4057 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing