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Staphylococcus aureus F98Y mutant dihydrofolate reductase complexed with NADPH and 2,4-diamino-5-[3-(3,4,5-trimethoxyphenyl)pent-1-ynyl]-6-methylpyrimidine (UCP115A)
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 2.73 54.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.218 α = 90 b = 79.218 β = 90 c = 108.746 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 1.77 32.72 89.4 0.068 0.068 1.4 11.1 17214 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 1.77 1.82 100 0.167 0.167 1.1 11.4 1374
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) 1.77 32.72 17214 17214 947 89.38 0.209 0.209 0.207 0.2081 0.245 0.2432 RANDOM 14.909
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 34.007 r_dihedral_angle_4_deg 19.949 r_dihedral_angle_3_deg 15.308 r_dihedral_angle_1_deg 6.546 r_angle_other_deg 3.31 r_scangle_it 2.328 r_scbond_it 1.45 r_angle_refined_deg 1.392 r_mcangle_it 1.112 r_mcbond_it 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.007 r_dihedral_angle_4_deg 19.949 r_dihedral_angle_3_deg 15.308 r_dihedral_angle_1_deg 6.546 r_angle_other_deg 3.31 r_scangle_it 2.328 r_scbond_it 1.45 r_angle_refined_deg 1.392 r_mcangle_it 1.112 r_mcbond_it 0.64 r_nbtor_refined 0.309 r_chiral_restr 0.242 r_symmetry_vdw_refined 0.2 r_nbd_refined 0.195 r_nbd_other 0.191 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.137 r_symmetry_vdw_other 0.096 r_nbtor_other 0.095 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1274 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 74
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