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Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001913, tetragonal 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 6.5 287 Morpheus screen condition b1: 10% (w/V) PEG 20,000, 20% (V/V) PEG MME 550: 30mM each sodium fluoride, sodium bromide, sodium iodide: 100m MES / imidazole HCl pH 6.5: MyulA.01062.a.B13.PS38558 at 7.98mg/ml + 2.5 mM NADP and SDDC-0001913 (bsi111354): tray 318490b1: cryo: direct: puck poq5-9
Crystal Properties Matthews coefficient Solvent content 2.98 58.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.97 α = 90 b = 58.97 β = 90 c = 130.34 γ = 90
Symmetry Space Group P 41 2 2
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 1.95 50 99.9 0.06 0.062 0.999 22.12 11.343 17565 42.213
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 1.95 2 100 0.561 0.587 0.977 4.11 11.842
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 1.95 43.73 1.37 17505 1804 99.87 0.185 0.1818 0.1835 0.213 0.2146 0 43.22
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 13.4382 f_angle_d 0.8881 f_chiral_restr 0.0554 f_bond_d 0.0068 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1209 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 80
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