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Crystal structure of the Streptomyces coelicolor TetR family protein ActR in complex with actinorhodin
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 8.5 293 15% PEG4000, 100 mM sodium acetate, 40 mM Tris, 25 mM KCl, 0.5 mM DTT, 15 mg/mL protein, 0.3 uL of 17 mM actinorhodin, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 49.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.88 α = 89.56 b = 79 β = 89.92 c = 107.19 γ = 89.88
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 2006-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 1.1 NSLS X12C
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 3.05 37.12 96 0.055 10.6 1.88 34551 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) 3.05 3.129 97 0.269 2.4 1.9
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 PDB entry 2OPT 3.05 37.12 29797 939 85.09 0.26077 0.25988 0.262 0.28835 0.28 RANDOM 59.765
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] -3.88 0.18 -0.08 7.5 0.21 -3.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.21 r_dihedral_angle_3_deg 23.368 r_dihedral_angle_4_deg 21.832 r_dihedral_angle_1_deg 7.129 r_angle_refined_deg 1.552 r_scangle_it 1.404 r_angle_other_deg 1.24 r_scbond_it 0.854 r_mcangle_it 0.619 r_mcbond_it 0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.21 r_dihedral_angle_3_deg 23.368 r_dihedral_angle_4_deg 21.832 r_dihedral_angle_1_deg 7.129 r_angle_refined_deg 1.552 r_scangle_it 1.404 r_angle_other_deg 1.24 r_scbond_it 0.854 r_mcangle_it 0.619 r_mcbond_it 0.338 r_nbd_other 0.328 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.293 r_nbd_refined 0.253 r_xyhbond_nbd_refined 0.186 r_nbtor_other 0.12 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.003 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 12788 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 400
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection d*TREK data reduction d*TREK data scaling CCP4 phasing Coot model building