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Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1439
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other in-house model
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 2.65 53.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.53 α = 90 b = 114.82 β = 108.25 c = 68.31 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 2017-02-08 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 1.62 57.41 97 0.049 0.059 0.032 0.998 11.9 3.3 103764
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 1.62 1.66 80.4 0.817 1.008 0.581 0.593 1.1 2.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT in-house model 1.62 57.41 98640 5120 96.89 0.16625 0.165 0.19039 0.2011 RANDOM 32.329
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] 2.88 -0.21 -0.54 -1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.091 r_dihedral_angle_4_deg 16.357 r_dihedral_angle_3_deg 13.318 r_long_range_B_other 6.991 r_long_range_B_refined 6.988 r_scangle_other 5.951 r_dihedral_angle_1_deg 5.18 r_scbond_it 4.076 r_scbond_other 4.074 r_mcangle_it 3.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.091 r_dihedral_angle_4_deg 16.357 r_dihedral_angle_3_deg 13.318 r_long_range_B_other 6.991 r_long_range_B_refined 6.988 r_scangle_other 5.951 r_dihedral_angle_1_deg 5.18 r_scbond_it 4.076 r_scbond_other 4.074 r_mcangle_it 3.595 r_mcangle_other 3.595 r_mcbond_it 2.69 r_mcbond_other 2.69 r_angle_refined_deg 1.817 r_angle_other_deg 1.079 r_chiral_restr 0.123 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 500 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing