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Crystal structure of Bacillus anthracis 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 2.55 51.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.884 α = 90 b = 77.884 β = 90 c = 67.431 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 2009-01-30 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 2.57 38.95 98.8 0.057 0.057 41.9 7.6 12154 12154 -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 2.57 2.64 98.1 0.154 0.154 14.3 7.7 898
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 2.57 38.95 12154 12154 622 98.76 0.20036 0.20036 0.19813 0.1969 0.24282 0.2391 RANDOM 19.69
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.823 r_dihedral_angle_3_deg 17.211 r_dihedral_angle_4_deg 16.082 r_dihedral_angle_1_deg 5.799 r_scangle_it 1.593 r_angle_refined_deg 1.264 r_scbond_it 1.016 r_mcangle_it 0.878 r_mcbond_it 0.496 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.823 r_dihedral_angle_3_deg 17.211 r_dihedral_angle_4_deg 16.082 r_dihedral_angle_1_deg 5.799 r_scangle_it 1.593 r_angle_refined_deg 1.264 r_scbond_it 1.016 r_mcangle_it 0.878 r_mcbond_it 0.496 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.183 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 2760 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 148
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling