☰ Navigation Tabs
tetracycline repressor class H, apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D5C PDB ENTRY 4D5C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 1.5 M LI2SO4, 0.1 M TRIS PH 8.5, CRYO: BRIEF SOAK IN 1.5 M LI2SO4, 0.1 M TRIS PH 8.5, 10% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.456 α = 90 b = 109.037 β = 90 c = 69.687 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD RIGAKU CCD MIRROR 2014-10-08 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 2.2 54 99 0.11 12.1 3.4 11494 28.8
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 2.2 2.34 96.2 0.49 2.7 2.7
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 4D5C 2.2 54.52 10985 511 99.06 0.19116 0.1885 0.1941 0.25146 0.2621 RANDOM 26.779
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] 0.23 -0.37 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.359 r_dihedral_angle_4_deg 18.994 r_dihedral_angle_3_deg 13.473 r_dihedral_angle_1_deg 4.986 r_mcangle_it 1.883 r_scbond_it 1.381 r_angle_refined_deg 1.287 r_mcbond_it 1.12 r_mcbond_other 1.115 r_angle_other_deg 0.781
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.359 r_dihedral_angle_4_deg 18.994 r_dihedral_angle_3_deg 13.473 r_dihedral_angle_1_deg 4.986 r_mcangle_it 1.883 r_scbond_it 1.381 r_angle_refined_deg 1.287 r_mcbond_it 1.12 r_mcbond_other 1.115 r_angle_other_deg 0.781 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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_it 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 1519 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing