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Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-226
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 2.7 54.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.72 α = 90 b = 120.17 β = 108.05 c = 68.17 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 2015-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 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 2.2 79.98 99.5 0.05 0.062 0.035 0.998 10.1 2.8 43570
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 2.2 2.32 99.7 0.364 0.447 0.256 0.902 2.5 2.9
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 79.98 41186 2191 99.06 0.1954 0.19303 0.1989 0.23959 0.2474 RANDOM 62.717
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] 6.6 0.32 -1.78 -4.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.772 r_dihedral_angle_4_deg 19.392 r_dihedral_angle_3_deg 16.37 r_long_range_B_other 11.169 r_long_range_B_refined 11.162 r_scangle_other 8.297 r_mcangle_it 7.871 r_mcangle_other 7.87 r_scbond_it 5.554 r_scbond_other 5.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.772 r_dihedral_angle_4_deg 19.392 r_dihedral_angle_3_deg 16.37 r_long_range_B_other 11.169 r_long_range_B_refined 11.162 r_scangle_other 8.297 r_mcangle_it 7.871 r_mcangle_other 7.87 r_scbond_it 5.554 r_scbond_other 5.553 r_dihedral_angle_1_deg 5.52 r_mcbond_it 5.431 r_mcbond_other 5.418 r_angle_refined_deg 1.612 r_angle_other_deg 1.042 r_chiral_restr 0.098 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 5260 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing