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Dihydrofolate reductase binding to NADPH and trimethoprim-tetramethylrhodamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NAQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 300 PEG 3350, Bis-Tris, magnesium dichloride
Crystal Properties Matthews coefficient Solvent content 2.72 54.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.995 α = 90 b = 79.995 β = 90 c = 106.073 γ = 120
Symmetry Space Group P 32 2 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 STFC Large Pixel Detector 2023-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97918 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.708 35.36 99.98 0.01336 1 27.09 3.3 43154
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 1.708 1.769 100 0.247 0.3493 0.247 0.837 2.45
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 1.708 35.36 43153 99.98 0.1712 0.1774 0.1956 0.1968 2004 34.35
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 16.3115 f_angle_d 1.1513 f_chiral_restr 0.0679 f_bond_d 0.0068 f_plane_restr 0.0055
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2492 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 211
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing