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L54A Mutant of E. coli Dihydrofolate Reductase Complexed with Nicotinamide Adenine Dinucleotide Phosphate (oxidized form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8VZ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 PEG 6000, calcium chloride, Tris
Crystal Properties Matthews coefficient Solvent content 2.2 44.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.597 α = 90 b = 58.812 β = 102.39 c = 71.276 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 16M 2025-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.9795 SSRL BL12-1
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 1.51 37.7 98.6 0.098 0.106 0.04 0.998 9.2 7 48391
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 1.51 1.53 93.9 1.401 1.534 0.61 0.741 5.9
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 1.51 37.7 1.35 48148 2424 98.2 0.2 0.198 0.2002 0.221 0.218
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 27.168 f_angle_d 1.318 f_chiral_restr 0.075 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2454 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 98
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing