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Crystal structure of Bacillus anthracis (Y102F) dihydrofolate reductase complexed with NADPH and (S)-2,4-diamino-5-(3-methoxy-3-(3,4,5-trimethoxyphenyl)prop-1-ynyl)-6-methylpyrimidine (UCP114A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EOB PDB entry 3EOB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.75 298 Initially grown in 25% PEG 10000, 0.1 M MES. Macroseeding in 10% PEG 10000, 0.1 M MES, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.56 51.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.858 α = 90 b = 77.858 β = 90 c = 67.526 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 2009-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9966 NSLS X25
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 2.08 42.68 100 0.161 0.161 26.1 7.3 23117 23117 -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 2.08 2.13 100 0.463 0.463 4.9 7.3 1697
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3EOB 2.08 42.68 23117 23117 1240 99.98 0.18453 0.18453 0.18299 0.1842 0.21293 0.2146 RANDOM 25.53
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 34.859 r_dihedral_angle_3_deg 14.879 r_dihedral_angle_4_deg 14.325 r_dihedral_angle_1_deg 6.039 r_scangle_it 2.412 r_scbond_it 1.659 r_angle_refined_deg 1.398 r_mcangle_it 1.129 r_mcbond_it 0.687 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.859 r_dihedral_angle_3_deg 14.879 r_dihedral_angle_4_deg 14.325 r_dihedral_angle_1_deg 6.039 r_scangle_it 2.412 r_scbond_it 1.659 r_angle_refined_deg 1.398 r_mcangle_it 1.129 r_mcbond_it 0.687 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.198 r_nbd_refined 0.19 r_symmetry_hbond_refined 0.144 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.095 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2758 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 148
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling