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TetR(D) in complex with oxytetracycline and magnesium.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TCT PDB ENTRY 2TCT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.45 M NA-MALONATE, 0.45 M NA-SUCCINATE, 0.1 M NA-CACODYLATE PH 5.55
Crystal Properties Matthews coefficient Solvent content 2.13 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.893 α = 90 b = 66.893 β = 90 c = 181.553 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 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2004-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 EMBL/DESY, HAMBURG X31
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 1.44 63.25 96.6 0.04 30.1 3.2 34700 -3 16.8
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 1.44 1.46 97.1 0.36 2.99 3.2
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 2TCT 1.44 63.25 34700 1826 96.64 0.17789 0.17651 0.1848 0.20473 0.2092 RANDOM 15.202
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] 0.47 0.47 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.787 r_dihedral_angle_4_deg 18.214 r_dihedral_angle_3_deg 13.432 r_dihedral_angle_1_deg 5.24 r_scangle_it 4.181 r_scbond_it 2.751 r_mcangle_it 1.945 r_angle_refined_deg 1.777 r_mcbond_it 1.154 r_angle_other_deg 1.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.787 r_dihedral_angle_4_deg 18.214 r_dihedral_angle_3_deg 13.432 r_dihedral_angle_1_deg 5.24 r_scangle_it 4.181 r_scbond_it 2.751 r_mcangle_it 1.945 r_angle_refined_deg 1.777 r_mcbond_it 1.154 r_angle_other_deg 1.011 r_mcbond_other 0.323 r_chiral_restr 0.172 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 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 1641 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing