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Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001565
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 D2: 10% w/v PEG 8000, 20% v/v ethylene glycol: 20mM of each 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol: 100mM MES/imidazole pH 6.5: MyulA.01062.a.B12.PS38539 and 15.75mg/ml + 2.5mM NADP and 4mM SDDC compound SDDC-0001565: tray: 317892d2: cryo: direct: puck: xhf8-2
Crystal Properties Matthews coefficient Solvent content 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.81 α = 90 b = 66.48 β = 92.014 c = 44.3 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 RIGAKU SATURN 944+ 2020-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.45 50 98.4 0.026 0.028 1 34.44 5.017 29111 18.119
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 1.45 1.49 91.6 0.182 0.222 0.952 5.25 2.561
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 1.45 44.27 1.37 29107 1955 98.36 0.1289 0.1267 0.1266 0.1585 0.159 0 15.47
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 14.7076 f_angle_d 1.084 f_chiral_restr 0.0791 f_plane_restr 0.0129 f_bond_d 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1244 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 75
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing Coot model building