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Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001912
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UWW NAD and P218-bound structure, PDB entry 6uww
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 287 Microlytic Morpheus screen, condition A5: 10% (w/V) PEG 20000, 20% (v/v) PEG MME 550: 30mM each MgCl2, CaCl2: 100mM MOPS / HEPES pH 7.5: MyulA.01062.a.B13.PS38558 at 7.98mg/ml + 2.5mM NADP + 2.5mM SDDC-0001912 (bsi111355): tray 318201 A5: cryo: direct: puck ucx6-7
Crystal Properties Matthews coefficient Solvent content 1.85 33.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.43 α = 90 b = 70.79 β = 111.48 c = 36.18 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 CCD RAYONIX MX-300 2020-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.25 35.4 99.4 0.051 0.06 0.999 14.22 3.641 37934 16.339
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 1.25 1.28 97.4 0.488 0.599 0.728 2.28 2.984
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE NAD and P218-bound structure, PDB entry 6uww 1.25 35.4 1.36 37929 1983 99.56 0.1357 0.1341 0.1342 0.1648 0.1647 0 16.2876
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1272 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 79
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing PHENIX model building Coot model building