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Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-008
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I15 PDB ENTRY 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; VAPOR DIFFUSION, HANGING DROP, 4 DEGREE
Crystal Properties Matthews coefficient Solvent content 2.86 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.36 α = 90 b = 115.74 β = 108.7 c = 68.41 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 CRL 2016-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.83 64.8 98 0.08 9.7 3.3 72702
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 1.83 1.88 98.4 1.17 1 3.5
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 PDB ENTRY 4I15 1.83 64.8 69149 3552 98.01 0.18496 0.1831 0.1915 0.22066 0.228 RANDOM 39.509
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] 3.13 -0.73 1.28 -3.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.158 r_dihedral_angle_3_deg 15.624 r_dihedral_angle_4_deg 14.832 r_dihedral_angle_1_deg 6.034 r_scangle_it 5.589 r_mcangle_it 4.329 r_scbond_it 3.867 r_mcbond_it 3.115 r_mcbond_other 3.112 r_angle_refined_deg 1.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.158 r_dihedral_angle_3_deg 15.624 r_dihedral_angle_4_deg 14.832 r_dihedral_angle_1_deg 6.034 r_scangle_it 5.589 r_mcangle_it 4.329 r_scbond_it 3.867 r_mcbond_it 3.115 r_mcbond_other 3.112 r_angle_refined_deg 1.771 r_angle_other_deg 1.063 r_chiral_restr 0.11 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other 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 383 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing