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Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor MAM846
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UWQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 PACT B4: 0.1M MIB (Sodium malonate dibasic monohydrate, Imidazole, Boric acid) pH 7, MyulA.01062.a.B11.PS38558 at 10 mg/mL. Tray: Tray358B4 MAM846, Puck: PUCK HR00407 pin15, Cryo: 20% PEG 300
Crystal Properties Matthews coefficient Solvent content 1.83 32.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.225 α = 90 b = 70.758 β = 111.28 c = 36.067 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 PIXEL DECTRIS PILATUS3 S 2M 2022-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0000 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.32 35.38 98.5 0.054 0.062 0.029 0.999 13.9 4.3 31584
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.32 1.34 91.7 0.555 0.655 0.339 0.734 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.32 35.38 1.36 31527 1583 98.32 0.1545 0.1528 0.1527 0.1842 0.1845
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 10.919 f_angle_d 1.203 f_chiral_restr 0.08 f_plane_restr 0.019 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1232 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 87
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing