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Staphylococcus aureus F98Y mutant dihydrofolate reductase complexed with NADPH and 2,4-Diamino-5-[3-(3-methoxy-5-phenylphenyl)but-1-ynyl]-6-methylpyrimidine
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, 150 mM Sodium acetate, 100 mM MES pH 6.5, 5 % Butyrlactone, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.74 55.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.134 α = 90 b = 79.134 β = 90 c = 109.169 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 2008-02-27 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 1.6 32.14 96.5 0.038 0.038 8.5 8.9 22505 22505 -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 1.6 1.66 87.2 0.212 0.212 2.5 1.5 1393
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 FOURIER SYNTHESIS THROUGHOUT Sa F98Y DHFR bound to Folate and NADPH (Dale et al., J.Mol.Biol. 1997, structure not deposited in the PDB). 1.6 32.14 22505 22505 1210 96.74 0.213 0.213 0.212 0.2105 0.244 0.2403 RANDOM 23.345
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 35.86 r_dihedral_angle_4_deg 20.897 r_dihedral_angle_3_deg 13.947 r_dihedral_angle_1_deg 6.083 r_scangle_it 2.877 r_scbond_it 2.014 r_angle_refined_deg 1.517 r_mcangle_it 1.436 r_mcbond_it 0.872 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.86 r_dihedral_angle_4_deg 20.897 r_dihedral_angle_3_deg 13.947 r_dihedral_angle_1_deg 6.083 r_scangle_it 2.877 r_scbond_it 2.014 r_angle_refined_deg 1.517 r_mcangle_it 1.436 r_mcbond_it 0.872 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.251 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.145 r_chiral_restr 0.1 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1274 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 75
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction Coot model building