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Structure of E. coli polIIIbeta with (Z)-5-(1-((4'-Fluorobiphenyl-4-yl)methoxyimino)butyl)-2,2-dimethyl-4,6-dioxocyclohexanecarbonitrile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MMI PDB ENTRY 1MMI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 100mM Na MES pH 6.0, 50-60mM CaCl2, 30%(v/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.42 49.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.176 α = 90 b = 66.519 β = 115.86 c = 83.117 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE MAR scanner 345 mm plate Mirrors 2007-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.9 25 94.8 0.243 13.8 57969 57969 -4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 87.9 2.7 3 5356
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 1MMI 1.9 24.69 54957 54957 2902 93.65 0.24621 0.24621 0.24249 0.2446 0.31701 0.3189 RANDOM 24.483
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] -0.67 -0.13 1.55 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.206 r_dihedral_angle_4_deg 20.834 r_dihedral_angle_3_deg 20.726 r_dihedral_angle_1_deg 9.034 r_scangle_it 5.44 r_scbond_it 3.424 r_angle_refined_deg 2.205 r_mcangle_it 2.172 r_mcbond_it 1.233 r_chiral_restr 0.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.206 r_dihedral_angle_4_deg 20.834 r_dihedral_angle_3_deg 20.726 r_dihedral_angle_1_deg 9.034 r_scangle_it 5.44 r_scbond_it 3.424 r_angle_refined_deg 2.205 r_mcangle_it 2.172 r_mcbond_it 1.233 r_chiral_restr 0.175 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5686 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 64
Software Software Software Name Purpose MAR345 data collection REFMAC refinement DENZO data reduction SCALEPACK data scaling