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Crystal structure of the CD40 and CD154 (CD40L) complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ALY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 12% PEG6000, 0.1M MOPS, 10% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.1 60.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.212 α = 90 b = 133.212 β = 90 c = 211.151 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 315 2006-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0050 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.2 114.961 93.7 0.102 0.102 8.9 2.6 24906 24906
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.69 97.6 0.351 0.351 0.506 0.308 2 2.5 3796
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1ALY 3.5 114.961 26756 24857 1209 92.9 0.245 0.245 0.2462 0.298 0.2998 RANDOM 68.3904
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] -2.61 -2.61 5.23
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.4 c_angle_deg 1.4 c_improper_angle_d 0.86 c_bond_d 0.01 c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9812 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 84
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing CNS refinement PDB_EXTRACT data extraction ADSC data collection