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Staphylococcus aureus H30N, F98Y 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 experimental model PDB 3FQO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 15% PEG 10,000, 150 mM sodium acetate, 100 mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.74 55.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.164 α = 90 b = 79.164 β = 90 c = 108.96 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 2009-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0809 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 2.41 37.22 95.01 0.04 0.04 1.1 10.4 7504 7504 3 3 15.689
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 2.41 2.472 100 0.074 0.074 0.8 10.1 560
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 Methods THROUGHOUT 3FQO 2.41 37.22 7504 7504 363 95.01 0.208 0.208 0.206 0.2069 0.261 0.2639 RANDOM 15.662
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] -0.01 -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.063 r_dihedral_angle_4_deg 20.893 r_dihedral_angle_3_deg 18.586 r_dihedral_angle_1_deg 7.585 r_scangle_it 2.709 r_scbond_it 1.777 r_angle_refined_deg 1.64 r_mcangle_it 1.314 r_mcbond_it 0.753 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.063 r_dihedral_angle_4_deg 20.893 r_dihedral_angle_3_deg 18.586 r_dihedral_angle_1_deg 7.585 r_scangle_it 2.709 r_scbond_it 1.777 r_angle_refined_deg 1.64 r_mcangle_it 1.314 r_mcbond_it 0.753 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.186 r_symmetry_hbond_refined 0.162 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1272 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction SCALEPACK data scaling Coot model building