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Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-048
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 3.17 61.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.052 α = 90 b = 114.73 β = 109.43 c = 63.8 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 2.1 70.28 99.8 0.103 0.125 0.069 0.992 7.1 3.1 58838
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 2.1 2.16 99.9 0.475 0.589 0.343 0.603 2.3 2.8
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 2.1 70.28 55845 2988 99.72 0.15911 0.15705 0.1716 0.19758 0.2092 RANDOM 32.055
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] 0.88 0.21 -1.26 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.538 r_dihedral_angle_3_deg 15.36 r_dihedral_angle_4_deg 14.729 r_long_range_B_other 7.287 r_long_range_B_refined 7.284 r_dihedral_angle_1_deg 5.826 r_scangle_other 5.754 r_scbond_it 3.827 r_scbond_other 3.817 r_mcangle_it 3.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.538 r_dihedral_angle_3_deg 15.36 r_dihedral_angle_4_deg 14.729 r_long_range_B_other 7.287 r_long_range_B_refined 7.284 r_dihedral_angle_1_deg 5.826 r_scangle_other 5.754 r_scbond_it 3.827 r_scbond_other 3.817 r_mcangle_it 3.713 r_mcangle_other 3.713 r_mcbond_it 2.598 r_mcbond_other 2.598 r_angle_refined_deg 1.834 r_angle_other_deg 1.122 r_chiral_restr 0.109 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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 5272 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 197
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing