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E. coli transcriptional regulator RUTR with dihydrouracil
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 200 nl of 10 mg/ml protein in 10 mM HEPES pH 7.5, 500 mM NaCl, 5 mM dihydrouracil was mixed with 200 nl 50 mM Ammonium Slufate, 50 mM BIS-TRIS, pH 6.5, 30% (v/v) Pentaerythirtol ethoxylate and suspended over a reservoir of 1.5M NaCl
Crystal Properties Matthews coefficient Solvent content 2.26 45.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.892 α = 88.37 b = 55.672 β = 88.8 c = 85.242 γ = 62.37
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 MARMOSAIC 300 mm CCD Beryllium Lenses 2014-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.27 50.01 97.5 0.056 14.6 2.2 81777 37742
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 2.27 2.31 91 0.55 1.67 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT 4JYK 2.27 50.01 35540 1827 97.51 0.19566 0.19407 0.1985 0.22539 0.2297 RANDOM 52.064
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] 2.31 -2.29 -1.92 -1.39 0.74 -2.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.706 r_dihedral_angle_3_deg 15.122 r_dihedral_angle_4_deg 14.276 r_dihedral_angle_1_deg 4.989 r_long_range_B_refined 4.03 r_long_range_B_other 3.975 r_scangle_other 2.578 r_mcangle_it 2.093 r_mcangle_other 2.093 r_scbond_it 1.558
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.706 r_dihedral_angle_3_deg 15.122 r_dihedral_angle_4_deg 14.276 r_dihedral_angle_1_deg 4.989 r_long_range_B_refined 4.03 r_long_range_B_other 3.975 r_scangle_other 2.578 r_mcangle_it 2.093 r_mcangle_other 2.093 r_scbond_it 1.558 r_scbond_other 1.558 r_angle_refined_deg 1.354 r_angle_other_deg 1.351 r_mcbond_it 1.326 r_mcbond_other 1.326 r_chiral_restr 0.078 r_gen_planes_refined 0.014 r_gen_planes_other 0.012 r_bond_refined_d 0.01 r_bond_other_d 0.007 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6133 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction PDB_EXTRACT data extraction HKL-3000 data scaling HKL-3000 phasing