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Human CD38 complexed with inhibitor 2 [4-[(2,6-dimethylbenzyl)amino]-2-methylquinoline-8-carboxamide]
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 7.5 295 Protein concentration 7mgs/ml. Crystals were grown from 23% PEG3350, 0.1mM BisTrisPropane at 22 deg C (2+2uL drops over a 500uL well). Crystals were soaked with 5mM inhibitor for 24 hours prior to data collection. Crystals were flash frozen in PFO.
Crystal Properties Matthews coefficient Solvent content 1.95 36.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.017 α = 90 b = 63.95 β = 90 c = 72.308 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD RIGAKU SATURN 944+ 2009-04-10 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 2.6 36.1 99 0.09 26 6.9 7323
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 2.6 2.66 100 0.47 4.7 7
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 2.6 36.1 7323 352 99.96 0.1942 0.1912 0.1945 0.2538 0.2561 RANDOM 48.013
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] 0.24 -0.53 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.21 r_dihedral_angle_4_deg 15.536 r_dihedral_angle_3_deg 13.605 r_dihedral_angle_1_deg 5.369 r_mcangle_it 2.751 r_mcbond_it 1.64 r_mcbond_other 1.637 r_angle_refined_deg 1.322 r_angle_other_deg 0.761 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.21 r_dihedral_angle_4_deg 15.536 r_dihedral_angle_3_deg 13.605 r_dihedral_angle_1_deg 5.369 r_mcangle_it 2.751 r_mcbond_it 1.64 r_mcbond_other 1.637 r_angle_refined_deg 1.322 r_angle_other_deg 0.761 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1903 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing