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Crystal structure of the ternary MTX NADPH complex of Bacillus anthracis dihydrofolate reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QK8 PDB entry 2QK8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 0.1 M Bis-Tris pH 5.5, 0.2 M CaCl2, 20% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.73 54.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.9 α = 90 b = 43.156 β = 119.31 c = 67.87 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm Mirrors 2008-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 0.90000 APS 14-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 20 93.8 0.131 8.6 3.1 10216 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.17 73.3 0.286 3 1.9 823
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 (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 PDB entry 2QK8 2.3 15.31 1 1 8332 8170 404 91.92 0.239 0.237 0.2372 0.277 0.2674 RANDOM 44.502
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] -0.03 -0.21 0.14 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.816 r_dihedral_angle_3_deg 21.993 r_dihedral_angle_4_deg 17.853 r_dihedral_angle_1_deg 8.102 r_scangle_it 2.87 r_angle_refined_deg 1.892 r_scbond_it 1.856 r_mcangle_it 1.234 r_mcbond_it 0.759 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.816 r_dihedral_angle_3_deg 21.993 r_dihedral_angle_4_deg 17.853 r_dihedral_angle_1_deg 8.102 r_scangle_it 2.87 r_angle_refined_deg 1.892 r_scbond_it 1.856 r_mcangle_it 1.234 r_mcbond_it 0.759 r_nbtor_refined 0.323 r_nbd_refined 0.24 r_symmetry_hbond_refined 0.201 r_xyhbond_nbd_refined 0.178 r_symmetry_vdw_refined 0.165 r_chiral_restr 0.126 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1280 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 81
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction BioCARS data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing