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STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE CD40 IN COMPLEX WITH 3H56-5 DAB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JMA CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF experimental model PDB 2UWI CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF experimental model PDB 2AW2 CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF experimental model PDB 1NCF CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 293 80mM Tris-HCl, pH 8.5, 1.6M Ammonium dihydrogen phosphate, 20% (v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 4.66 73.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.6 α = 90 b = 158.3 β = 90 c = 200.7 γ = 90
Symmetry Space Group I 2 2 2
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 RIGAKU SATURN 92 MICROMAX CONFOCAL 2009-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
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 3.3 50 99.8 0.137 33.7 42.5 37772 53.11
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 3.3 3.36 99.8 0.439 12.5 43.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF 3.3 29.04 34308 953 90.8 0.269 0.268 0.298 0.2986 RANDOM 79.59
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] -1.3656 -7.672 9.0375
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 23.92 t_omega_torsion 3.4 t_angle_deg 1.43 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 23.92 t_omega_torsion 3.4 t_angle_deg 1.43 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8271 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 20
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing