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Catalysis associated conformational changes revealed by human cd38 complexed with a non-hydrolyzable substrate analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O3T PDB entry 2O3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 300 100 mM MES, pH 6.0, and 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.31 46.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.891 α = 105.34 b = 53.195 β = 91.96 c = 65.636 γ = 94.94
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 210 2006-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.976 CHESS A1
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 1.7 30 92.7 0.082 3.6 58649 54368 3 3
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 1.7 1.76 71 0.318 2.73 2.5 4146
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 (All) 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 PDB entry 2O3T 1.71 28.41 54283 51521 2762 100 0.19239 0.19239 0.1907 0.2796 0.22359 0.3053 RANDOM 30.691
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] -0.82 0.29 0.39 0.02 1.13 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.562 r_dihedral_angle_4_deg 15.157 r_dihedral_angle_3_deg 14.443 r_dihedral_angle_1_deg 5.342 r_scangle_it 2.868 r_scbond_it 1.801 r_angle_refined_deg 1.182 r_mcangle_it 1.065 r_mcbond_it 0.627 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.562 r_dihedral_angle_4_deg 15.157 r_dihedral_angle_3_deg 14.443 r_dihedral_angle_1_deg 5.342 r_scangle_it 2.868 r_scbond_it 1.801 r_angle_refined_deg 1.182 r_mcangle_it 1.065 r_mcbond_it 0.627 r_nbtor_refined 0.309 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.126 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4100 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing