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Staphylococcus aureus F98Y mutant dihydrofolate reductase complexed with NADPH and 2,4-diamino-5-[3-(2,5-dimethoxyphenyl)prop-1-ynyl]-6-ethylpyrimidine (UCP120B)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Sa F98Y DHFR bound to Folate and NADPH (Dale et al., J.Mol.Biol. 1997, structure not deposited in the PDB)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 15% PEG 10000, 150mM Sodium acetate, 100mM MES pH 6.5, 5% Butyrlactone, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.68 54.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.866 α = 90 b = 78.866 β = 90 c = 107.825 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77.2 CCD ADSC QUANTUM 315 2008-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.080900 NSLS X29A
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 2.09 42.33 99.1 0.064 0.064 5 9.4 11685 3
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 2.09 2.18 100 0.406 0.406 3.8 9.5 838
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 DIFFERENCE FOURIER THROUGHOUT Sa F98Y DHFR bound to Folate and NADPH (Dale et al., J.Mol.Biol. 1997, structure not deposited in the PDB) 2.09 42.33 11685 11685 608 99.1 0.218 0.218 0.216 0.2151 0.261 0.256 RANDOM 30.258
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] -0.02 -0.01 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.263 r_dihedral_angle_4_deg 18.202 r_dihedral_angle_3_deg 14.626 r_dihedral_angle_1_deg 6.099 r_scangle_it 1.91 r_angle_refined_deg 1.395 r_scbond_it 1.189 r_mcangle_it 1.037 r_mcbond_it 0.583 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.263 r_dihedral_angle_4_deg 18.202 r_dihedral_angle_3_deg 14.626 r_dihedral_angle_1_deg 6.099 r_scangle_it 1.91 r_angle_refined_deg 1.395 r_scbond_it 1.189 r_mcangle_it 1.037 r_mcbond_it 0.583 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.197 r_symmetry_hbond_refined 0.19 r_nbd_refined 0.184 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.086 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1274 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 71
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection Coot model building CCP4 phasing