☰ Navigation Tabs
Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-055
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 2.68 54.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.78 α = 90 b = 116.48 β = 108.32 c = 68.61 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 2016-04-28 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) 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 2.03 79.57 99.7 0.065 0.077 0.041 0.999 11.5 3.4 55071
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 2.03 2.08 99.7 1.17 1.395 0.751 0.592 1.1 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 2.03 79.57 52428 2642 99.69 0.18272 0.18014 0.1907 0.23342 0.2243 RANDOM 48.062
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] 3.82 -0.78 1.7 -4.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.543 r_dihedral_angle_3_deg 16.125 r_dihedral_angle_4_deg 14.446 r_long_range_B_other 8.093 r_long_range_B_refined 8.092 r_scangle_other 6.241 r_dihedral_angle_1_deg 6.062 r_mcangle_it 5.119 r_mcangle_other 5.118 r_scbond_it 4.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.543 r_dihedral_angle_3_deg 16.125 r_dihedral_angle_4_deg 14.446 r_long_range_B_other 8.093 r_long_range_B_refined 8.092 r_scangle_other 6.241 r_dihedral_angle_1_deg 6.062 r_mcangle_it 5.119 r_mcangle_other 5.118 r_scbond_it 4.159 r_scbond_other 4.158 r_mcbond_it 3.568 r_mcbond_other 3.565 r_angle_refined_deg 1.465 r_angle_other_deg 1.32 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 336 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing