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Crystal structure of dihydrofolate reductase from Mycobacterium ulcerans with SDDC-0001565 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DF7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 287 MyulA.01062.a.B13.PS38558 at 7.98mg/ml, incubated with 3 mM SDDC-0001565 and 3 mM NADP, mixed 1:1 with 100mM Bis-Tris:HCl pH6.5, 25% (w/v) PEG3350, 7.98mg/mL MyulA.01062.a.B13.PS38558. Tray: 311137d2, puck: sxq1-11, cryoprotected with 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 1.83 32.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.29 α = 90 b = 70.75 β = 110.991 c = 35.99 γ = 90
Symmetry Space Group P 1 21 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 2018-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.5 50 98.3 0.036 0.042 0.999 21.55 3.701 21600 21.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 96.3 0.328 0.386 0.954 3.75 3.613
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1df7 1.5 35.38 1.38 21592 1992 98.46 0.1358 0.1314 0.132 0.1788 0.1788 17.47
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.2802 f_angle_d 0.9167 f_chiral_restr 0.0522 f_plane_restr 0.006 f_bond_d 0.0055
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1252 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 82
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction