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Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-053
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 3.15 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.516 α = 90 b = 115.07 β = 109.39 c = 63.78 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 2015-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 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 1.9 69.57 99.7 0.091 0.11 0.061 0.995 7.2 3.1 78709
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 1.9 1.94 99.9 0.626 0.748 0.405 0.475 2 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 1.9 69.57 74823 3878 99.69 0.16703 0.16547 0.1798 0.1972 0.209 RANDOM 30.256
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] 1.56 -0.14 -1.16 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.504 r_dihedral_angle_4_deg 16.296 r_dihedral_angle_3_deg 15.357 r_long_range_B_refined 7.907 r_long_range_B_other 7.906 r_scangle_other 6.111 r_dihedral_angle_1_deg 5.854 r_scbond_it 4.061 r_scbond_other 4.06 r_mcangle_it 3.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.504 r_dihedral_angle_4_deg 16.296 r_dihedral_angle_3_deg 15.357 r_long_range_B_refined 7.907 r_long_range_B_other 7.906 r_scangle_other 6.111 r_dihedral_angle_1_deg 5.854 r_scbond_it 4.061 r_scbond_other 4.06 r_mcangle_it 3.893 r_mcangle_other 3.893 r_mcbond_it 2.737 r_mcbond_other 2.735 r_angle_refined_deg 1.713 r_angle_other_deg 1.43 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 5272 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing