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Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-039
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 2.76 55.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.6 α = 90 b = 115.13 β = 108.12 c = 68.63 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 2016-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97623 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.01 57.56 99.4 0.094 0.997 9.6 3.4 55896
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 2.01 2.06 99.4 1.203 1.3 3.4
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 2.01 57.06 53212 2682 99.37 0.19748 0.19543 0.204 0.23748 0.2435 RANDOM 48.762
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] 6.71 -1.1 -0.85 -4.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.528 r_dihedral_angle_3_deg 15.815 r_dihedral_angle_4_deg 15.351 r_long_range_B_refined 8.692 r_long_range_B_other 8.689 r_scangle_other 6.685 r_dihedral_angle_1_deg 5.847 r_mcangle_it 5.437 r_mcangle_other 5.436 r_scbond_it 4.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.528 r_dihedral_angle_3_deg 15.815 r_dihedral_angle_4_deg 15.351 r_long_range_B_refined 8.692 r_long_range_B_other 8.689 r_scangle_other 6.685 r_dihedral_angle_1_deg 5.847 r_mcangle_it 5.437 r_mcangle_other 5.436 r_scbond_it 4.5 r_scbond_other 4.492 r_mcbond_it 3.692 r_mcbond_other 3.692 r_angle_refined_deg 1.693 r_angle_other_deg 1.3 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.006 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 335 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Coot model building