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Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1335
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I15
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 pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.876 α = 90 b = 114.424 β = 108.36 c = 68.232 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 PILATUS 6M-F 2018-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 1.96 64.76 99.8 0.098 0.117 0.063 0.992 6 3.3 59811
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 1.96 2.01 99.9 0.704 0.838 0.45 0.595 1.3 3.3
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 4I15 1.96 57.28 55439 2895 97.02 0.2021 0.19988 0.2071 0.24379 0.2498 RANDOM 40.075
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] 4.41 -0.51 -2.12 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.907 r_dihedral_angle_3_deg 15.05 r_dihedral_angle_4_deg 13.904 r_long_range_B_refined 6.768 r_long_range_B_other 6.767 r_dihedral_angle_1_deg 5.858 r_scangle_other 5.134 r_mcangle_it 4.135 r_mcangle_other 4.135 r_scbond_it 3.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.907 r_dihedral_angle_3_deg 15.05 r_dihedral_angle_4_deg 13.904 r_long_range_B_refined 6.768 r_long_range_B_other 6.767 r_dihedral_angle_1_deg 5.858 r_scangle_other 5.134 r_mcangle_it 4.135 r_mcangle_other 4.135 r_scbond_it 3.333 r_scbond_other 3.333 r_mcbond_it 2.795 r_mcbond_other 2.791 r_angle_refined_deg 1.247 r_angle_other_deg 0.962 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 433 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing