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Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001914, orthorhombic crystal from
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 7.5 287 Morpheus screen condition a9: 10% (w/V) PEG 20,000, 20% (V/V) PEG MME 550: 30mM each magnesium chloride, calcium chloride: 100m bicine / trizma base HCl pH 7.5: MyulA.01062.a.B13.PS38588 at 7.98mg/mll + 2.5 mM NADP and SDDC-0001914 (bsi111353): tray 318487a9: cryo: direct: puck poq5-9
Crystal Properties Matthews coefficient Solvent content 2.83 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.03 α = 90 b = 82.79 β = 90 c = 133.12 γ = 90
Symmetry Space Group I 21 21 21
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 2020-10-22 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 1.55 50 99.9 0.063 0.069 0.999 17.91 6.121 62683 22.779
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 1.55 1.59 100 0.583 0.638 0.873 3.24 6.093
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 1.55 39.11 1.35 62674 1932 99.86 0.1568 0.1561 0.1563 0.1778 0.1778 0 20.91
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 13.5725 f_angle_d 0.9764 f_chiral_restr 0.0607 f_plane_restr 0.0089 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2428 Nucleic Acid Atoms Solvent Atoms 523 Heterogen Atoms 158
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