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Crystal Structure of Dihydrofolate reductase from Mycobacterium kansasii in complex with NADP and inhibitor P218
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DF7 pdb entry 1df7 as per Morda
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 287 Microlytics Morpheus screen, condition E4: 12.5% (w/V) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (V/V) MPD: 30mM of each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethyleneglycol: 100mM MES/imidazole pH 6.5. MykaA.01062.a.B1.PS38569 at 5.22mg/ml + 2mM each NADP and P218: tray 309622 e4: cryo: direct: puck kdu7-7
Crystal Properties Matthews coefficient Solvent content 2.38 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.1 α = 90 b = 66.25 β = 90 c = 86.12 γ = 90
Symmetry Space Group P 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 Beryllium Lenses 2020-08-06 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 2.05 50 99.7 0.06 0.067 0.999 14.45 5.108 22844 42.831
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 2.05 2.1 99.3 0.598 0.692 0.826 1.99 3.947
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 pdb entry 1df7 as per Morda 2.05 35.39 1.34 22676 1978 99 0.216 0.2109 0.2114 0.2683 0.2683 0 51.07
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 15.9948 f_angle_d 0.9194 f_chiral_restr 0.052 f_plane_restr 0.0095 f_bond_d 0.0073
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2597 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 156
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing PHENIX model building Coot model building