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Human CD38 complexed with inhibitor 1 [6-fluoro-2-methyl-4-[(2,3,6-trichlorobenzyl)amino]quinoline-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 was 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 36.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.298 α = 90 b = 64.424 β = 90 c = 72.832 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+ 2011-01-25 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 2.8 34.8 98 0.09 29 6.6 5790
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 2.8 2.87 99.5 0.59 4.8 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 2.8 34.8 5790 293 98.45 0.1899 0.1863 0.187 0.2634 0.2527 RANDOM 53.927
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] 0.01 -0.12 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.038 r_dihedral_angle_4_deg 15.953 r_dihedral_angle_3_deg 14.175 r_dihedral_angle_1_deg 5.427 r_mcangle_it 1.961 r_angle_refined_deg 1.239 r_mcbond_it 1.202 r_mcbond_other 1.191 r_angle_other_deg 0.792 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.038 r_dihedral_angle_4_deg 15.953 r_dihedral_angle_3_deg 14.175 r_dihedral_angle_1_deg 5.427 r_mcangle_it 1.961 r_angle_refined_deg 1.239 r_mcbond_it 1.202 r_mcbond_other 1.191 r_angle_other_deg 0.792 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1886 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing