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Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-0769
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
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.621 α = 90 b = 115.344 β = 108.32 c = 68.585 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 2016-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 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 1.942 65.11 93.3 0.106 0.127 0.069 0.991 9.2 3.3 58668
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 1.942 1.976 96.3 0.863 1.026 0.55 0.66 2.1 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4I15 1.942 65.11 55658 2944 93.22 0.18126 0.17894 0.22457 0.2304 RANDOM 30.539
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] 3.83 -1.19 -0.38 -2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.269 r_dihedral_angle_4_deg 15.122 r_dihedral_angle_3_deg 14.869 r_long_range_B_refined 6.641 r_long_range_B_other 6.614 r_dihedral_angle_1_deg 5.921 r_scangle_other 4.668 r_mcangle_it 3.44 r_mcangle_other 3.44 r_scbond_it 3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.269 r_dihedral_angle_4_deg 15.122 r_dihedral_angle_3_deg 14.869 r_long_range_B_refined 6.641 r_long_range_B_other 6.614 r_dihedral_angle_1_deg 5.921 r_scangle_other 4.668 r_mcangle_it 3.44 r_mcangle_other 3.44 r_scbond_it 3.05 r_scbond_other 3.049 r_mcbond_it 2.253 r_mcbond_other 2.252 r_angle_refined_deg 1.5 r_angle_other_deg 1.363 r_chiral_restr 0.077 r_bond_refined_d 0.008 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 427 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing Coot model building