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Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-356
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
Crystal Properties Matthews coefficient Solvent content 2.65 53.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.69 α = 90 b = 119.26 β = 108.38 c = 67.97 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 2017-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 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 1.96 33.91 99.5 0.046 0.055 0.03 0.999 13.6 3.4 60184
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 99.8 0.937 1.11 0.589 0.604 1.4 3.4
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 33.91 57112 3068 99.45 0.19221 0.18981 0.2032 0.23697 0.2405 RANDOM 52.319
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] 3.64 0.07 -0.56 -2.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.987 r_dihedral_angle_3_deg 16.81 r_dihedral_angle_4_deg 16.444 r_long_range_B_refined 9.105 r_long_range_B_other 9.105 r_scangle_other 7.118 r_mcangle_other 6.399 r_mcangle_it 6.398 r_dihedral_angle_1_deg 6.276 r_scbond_it 5.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.987 r_dihedral_angle_3_deg 16.81 r_dihedral_angle_4_deg 16.444 r_long_range_B_refined 9.105 r_long_range_B_other 9.105 r_scangle_other 7.118 r_mcangle_other 6.399 r_mcangle_it 6.398 r_dihedral_angle_1_deg 6.276 r_scbond_it 5.002 r_scbond_other 5.001 r_mcbond_it 4.658 r_mcbond_other 4.655 r_angle_refined_deg 1.796 r_angle_other_deg 1.078 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 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 5252 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing