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Bacillus anthracis Dihydrofolate Reductase bound to propargyl-linked TMP analog, UCP120J
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E0B PDB entry 3E0B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 300 initial hits were grown at room temperature by hanging drop diffusion in 21.0% (w/v) PEG 10,000, 0.1 M MES, pH 6.75, at an equal ratio of protein to crystallization solution. Microseeding was used to obtain isolated crystals in 11% PEG 10,000 and 0.1 MES, pH 6.75 at a protein concentration of 8 mg/mL, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.61 52.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.187 α = 90 b = 78.187 β = 90 c = 67.094 γ = 90
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 2008-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.979505 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 1.9 30.83 99.9 0.073 0.073 25.6 7.4 30364 30364 5 5
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 1.9 1.95 99.9 0.397 0.397 3.5 6.5 2228
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3E0B 1.9 30.8 3 3096 30364 1619 99.94 0.22311 0.19161 0.18998 0.22311 0.2275 RANDOM 20.748
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 33.594 r_dihedral_angle_3_deg 11.913 r_dihedral_angle_4_deg 10.003 r_dihedral_angle_1_deg 5.526 r_scangle_it 1.873 r_angle_refined_deg 1.131 r_scbond_it 1.085 r_mcangle_it 0.94 r_mcbond_it 0.496 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.594 r_dihedral_angle_3_deg 11.913 r_dihedral_angle_4_deg 10.003 r_dihedral_angle_1_deg 5.526 r_scangle_it 1.873 r_angle_refined_deg 1.131 r_scbond_it 1.085 r_mcangle_it 0.94 r_mcbond_it 0.496 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2760 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 150
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling