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Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor MAM787
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 6.5 291 Morpheus F4: 12.5% PDB 1000, 12.5% PEG 3350, 12.5% MPD 0.02M of each monosaccharide (d-glucose, d-mannose, d-galactose, l-fucose, d-xylose, N-acetyld-glucosamine), 0.1M MES/imidazole pH 6.5 , MyulA.01062.a.B13.PS38558 at 10 mg/mL. Tray: Tray 355D3/ MAM738 +NADP, Puck: CPS5110_06, Cryo: Direct
Crystal Properties Matthews coefficient Solvent content 2.21 44.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.698 α = 90 b = 66.374 β = 91.44 c = 44.146 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 EIGER2 XE 9M 2022-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.97949 NSLS-II 19-ID
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 1.1 44.13 98.3 0.024 0.026 0.01 1 30.2 6.6 65812
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 1.1 1.12 76.2 0.236 0.269 0.125 0.954 4.3
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 1.1 23.78 1.21 65775 3297 98.25 0.1263 0.1254 0.1368 0.144 0.1512
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 12.311 f_angle_d 1.053 f_chiral_restr 0.069 f_plane_restr 0.013 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1246 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 77
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing