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Crystal structure of the Streptomyces coelicolor TetR family protein ActR in complex with (S)-DNPA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OPT pdb entry 2OPT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 14% PEG4000, 91mM sodium acetate, 45mM Bis-Tris, 23mM KCl, 9.1mM taurine, 4.6mM Tris, 0.45mM DTT and, after dehydration, less than 100 ug (S)-DNPA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.969 α = 90 b = 79.396 β = 90 c = 103.453 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 4 collimating and focusing mirrors 2006-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 1.1 NSLS X8C
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 2.3 49.23 92.1 0.047 17.6 4.63 19458 1 1
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) 2.3 2.38 95.7 0.211 4.3 4.47
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 (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 2OPT 2.3 41.85 19458 14054 743 70.04 0.24605 0.24392 0.2607 0.28703 0.3115 RANDOM 83.439
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] -5 5.96 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.099 r_dihedral_angle_4_deg 23.685 r_dihedral_angle_3_deg 21.245 r_angle_other_deg 9.262 r_dihedral_angle_1_deg 6.666 r_scangle_it 2.81 r_mcangle_it 2.404 r_scbond_it 1.829 r_mcbond_it 1.354 r_angle_refined_deg 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.099 r_dihedral_angle_4_deg 23.685 r_dihedral_angle_3_deg 21.245 r_angle_other_deg 9.262 r_dihedral_angle_1_deg 6.666 r_scangle_it 2.81 r_mcangle_it 2.404 r_scbond_it 1.829 r_mcbond_it 1.354 r_angle_refined_deg 0.92 r_symmetry_hbond_refined 0.431 r_nbd_other 0.419 r_symmetry_vdw_refined 0.343 r_nbtor_refined 0.335 r_nbd_refined 0.3 r_xyhbond_nbd_refined 0.269 r_nbtor_other 0.245 r_chiral_restr 0.078 r_gen_planes_refined 0.012 r_bond_refined_d 0.007 r_bond_other_d 0.002 r_gen_planes_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 3082 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection d*TREK data reduction d*TREK data scaling CCP4 phasing Coot model building