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Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-637
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 2.59 52.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.98 α = 90 b = 113.48 β = 107.89 c = 68.22 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 2012-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9173 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 56.74 95.9 0.069 0.1 0.053 11 3.5 40120
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 87.1 0.549 0.76 0.402 2 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 4I15 2.2 56.74 38109 2011 95.71 0.171 0.16896 0.1766 0.20859 0.2146 RANDOM 39.393
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] 4.65 -1.77 -1.37 -1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.245 r_dihedral_angle_4_deg 16.872 r_dihedral_angle_3_deg 15.723 r_long_range_B_refined 7.687 r_long_range_B_other 7.68 r_scangle_other 6.038 r_dihedral_angle_1_deg 5.353 r_mcangle_it 4.827 r_mcangle_other 4.827 r_scbond_it 3.879
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.245 r_dihedral_angle_4_deg 16.872 r_dihedral_angle_3_deg 15.723 r_long_range_B_refined 7.687 r_long_range_B_other 7.68 r_scangle_other 6.038 r_dihedral_angle_1_deg 5.353 r_mcangle_it 4.827 r_mcangle_other 4.827 r_scbond_it 3.879 r_scbond_other 3.878 r_mcbond_other 3.156 r_mcbond_it 3.155 r_angle_refined_deg 1.622 r_angle_other_deg 1.023 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 5246 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing