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Structural Analysis of a Holo Enzyme Complex of Mouse Dihydrofolate Reductase with NADPH and a Ternary Complex wtih the Potent and Selective Inhibitor 2,4-Diamino-6-(2'-hydroxydibenz[b,f]azepin-5-yl)methylpteridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FZJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.15 M Tris, pH 8.3, 75 mM Na cacodylate, pH 6.5, 21% PEG 4K, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.29 46.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.482 α = 90 b = 61.3 β = 117.23 c = 43.589 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 200 CCD MAR CCD 130 mm 2006-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 1.00 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.4 31.61 98.3 0.083 0.06 5.3 3.7 38237 35455 1 1 25
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.45 15.2 0.3 0.02 31.5 2 2589
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 THROUGHOUT 2fzj 1.4 31.61 1 1 35455 35455 1851 97.57 0.22 0.20072 0.19882 0.2295 0.23573 0.252 RANDOM 19.942
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 r_dihedral_angle_2_deg 33.902 r_dihedral_angle_4_deg 14.526 r_dihedral_angle_3_deg 14.215 r_dihedral_angle_1_deg 5.633 r_scangle_it 2.963 r_scbond_it 1.976 r_angle_refined_deg 1.682 r_mcangle_it 1.375 r_mcbond_it 0.831 r_chiral_restr 0.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.902 r_dihedral_angle_4_deg 14.526 r_dihedral_angle_3_deg 14.215 r_dihedral_angle_1_deg 5.633 r_scangle_it 2.963 r_scbond_it 1.976 r_angle_refined_deg 1.682 r_mcangle_it 1.375 r_mcbond_it 0.831 r_chiral_restr 0.374 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.243 r_nbd_refined 0.21 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.167 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1513 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection MOSFLM data reduction SCALA data scaling MOLREP phasing