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Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1086
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 20% PEG 3350, 0.4 M sodium formate, 0.3 M guanidine, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 2.65 53.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.102 α = 90 b = 116.385 β = 108.67 c = 68.31 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M CRL 2016-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.31 57.1 97.1 0.051 0.061 0.033 0.999 12.3 3.4 36029
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.31 2.34 96.7 0.501 0.592 0.312 0.91 2.5 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 2.31 57.1 34309 1717 97.08 0.17218 0.16909 0.1832 0.23191 0.2256 RANDOM 66.101
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] 4.58 -0.71 1.73 -4.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.826 r_dihedral_angle_4_deg 18.035 r_dihedral_angle_3_deg 17.343 r_long_range_B_refined 10.491 r_long_range_B_other 10.485 r_scangle_other 7.923 r_mcangle_it 7.381 r_mcangle_other 7.38 r_dihedral_angle_1_deg 6.17 r_scbond_it 5.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.826 r_dihedral_angle_4_deg 18.035 r_dihedral_angle_3_deg 17.343 r_long_range_B_refined 10.491 r_long_range_B_other 10.485 r_scangle_other 7.923 r_mcangle_it 7.381 r_mcangle_other 7.38 r_dihedral_angle_1_deg 6.17 r_scbond_it 5.338 r_scbond_other 5.336 r_mcbond_it 5.053 r_mcbond_other 5.052 r_angle_refined_deg 1.607 r_angle_other_deg 1.032 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5260 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling REFMAC phasing