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Tet-repressor class D T103A with doxycycline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O7O PDB ENTRY 2O7O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 HANGING DROP VAPOR DIFFUSION WITH 2 UL (14 MG/ML PROTEIN) AND 2 UL (0.6 M NACL, 15 % PEG 4000, 0.1 M MES PH 6.5). CRYSTAL WAS CRYOCOOLED WITH PARAFFIN OIL AS CRYOPROTECTANT.
Crystal Properties Matthews coefficient Solvent content 2.17 43.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.888 α = 90 b = 67.888 β = 90 c = 180.438 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 100 CCD RIGAKU-MSC MIRRORS 2007-03-29 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 1.8 33 98.4 0.07 13 9.17 19733 -3 38
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 1.8 1.86 88.6 0.54 1.7 3.43
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 2O7O 1.85 32.87 17378 912 98.75 0.238 0.23584 0.2427 0.27908 0.288 RANDOM 45.851
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] 0.87 0.87 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.936 r_dihedral_angle_4_deg 23.89 r_dihedral_angle_3_deg 14.161 r_dihedral_angle_1_deg 6.531 r_scangle_it 4.13 r_scbond_it 2.785 r_angle_refined_deg 1.854 r_mcangle_it 1.796 r_angle_other_deg 1.156 r_mcbond_it 1.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.936 r_dihedral_angle_4_deg 23.89 r_dihedral_angle_3_deg 14.161 r_dihedral_angle_1_deg 6.531 r_scangle_it 4.13 r_scbond_it 2.785 r_angle_refined_deg 1.854 r_mcangle_it 1.796 r_angle_other_deg 1.156 r_mcbond_it 1.076 r_mcbond_other 0.321 r_chiral_restr 0.155 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_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 1639 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling REFMAC phasing