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Crystal structure of human CD38 in complex with hydrolysed compound JMS713
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YH3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 298 0.1M sodium acetate pH4.0, 0.2M ammonium acetate, 3% isopropanol, 15% PEG10000
Crystal Properties Matthews coefficient Solvent content 2.26 45.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.69 α = 108.58 b = 54.128 β = 90.98 c = 63.319 γ = 93.98
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 315r 2012-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97852 SSRF BL17U
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 2.05 50 97.6 0.046 14.8 3.9 31966
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 2.05 2.12 97.3 0.528 3.9 3188
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 1YH3 2.05 47.12 31950 1638 97.3 0.1996 0.198 0.2042 0.227 0.23 RANDOM 67.282
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] -3.45 -2 -0.3 2.67 1.53 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.842 r_dihedral_angle_4_deg 16.58 r_dihedral_angle_3_deg 16.171 r_dihedral_angle_1_deg 5.955 r_mcangle_it 2.253 r_mcbond_it 1.52 r_mcbond_other 1.52 r_angle_refined_deg 1.426 r_angle_other_deg 1.127 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.842 r_dihedral_angle_4_deg 16.58 r_dihedral_angle_3_deg 16.171 r_dihedral_angle_1_deg 5.955 r_mcangle_it 2.253 r_mcbond_it 1.52 r_mcbond_other 1.52 r_angle_refined_deg 1.426 r_angle_other_deg 1.127 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3946 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 66
Software Software Software Name Purpose Blu-Ice data collection HKL-2000 data scaling PHASER phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction