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Tet repressor class D complexed with cobalt and tetracycline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FJ1 PDB ENTRY 2FJ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 HANGING DROP VAPOR DIFFUSION WITH 2 UL (18 MG/ML PROTEIN) AND 2 UL (0.8 M AS, 50 MM TRIS/CL PH 7.5, 200 MM NACL, 5 MM COCL2). CRYSTAL WAS CRYOCOOLED WITH PARAFFIN OIL AS CRYOPROTECTANT. CRYSTAL SIZE WAS 0.6 X 0.6 X 0.2 MM
Crystal Properties Matthews coefficient Solvent content 2.2 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.014 α = 90 b = 67.014 β = 90 c = 180.806 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD SATURN MIRRORS 2007-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 1.62 62 85.4 0.08 12.8 7 21642 31
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 1.62 1.68 19 0.65 0.8 1.26
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 2FJ1 1.62 62.87 21642 1143 85.4 0.247 0.245 0.2407 0.297 0.2894 RANDOM 30.56
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 0.67 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.222 r_dihedral_angle_4_deg 15.805 r_dihedral_angle_3_deg 14.981 r_dihedral_angle_1_deg 5.25 r_scangle_it 3.756 r_scbond_it 2.839 r_angle_refined_deg 1.783 r_mcangle_it 1.556 r_mcbond_it 1.059 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.222 r_dihedral_angle_4_deg 15.805 r_dihedral_angle_3_deg 14.981 r_dihedral_angle_1_deg 5.25 r_scangle_it 3.756 r_scbond_it 2.839 r_angle_refined_deg 1.783 r_mcangle_it 1.556 r_mcbond_it 1.059 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.26 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.194 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.149 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1590 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling PHASER phasing