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TetR(D) H100A mutant in complex with anhydrotetracycline and magnesium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D7M PDB ENTRY 4D7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 295 0.4 M (NH4)2SO4, 0.7 M LI2SO4, 0.1 M SODIUM CITRATE, 1 MM 5A,6-ANHYDROTETRACYCLINE, 7.5 MM MGCL2 AT 295 K
Crystal Properties Matthews coefficient Solvent content 2.14 42.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.557 α = 90 b = 66.557 β = 90 c = 179.681 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 RAYONIX SX-165mm MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 1.9 62 97.1 0.05 24.5 4.8 15800 -3 37.4
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 1.9 1.93 99.2 0.67 2.5 4.5
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 4D7M 1.9 62.02 15187 808 98.04 0.21695 0.21474 0.2215 0.26545 0.2718 RANDOM 48.078
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] 2.78 2.78 -5.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.422 r_dihedral_angle_4_deg 17.052 r_dihedral_angle_3_deg 14.197 r_dihedral_angle_1_deg 4.808 r_mcangle_it 2.65 r_scbond_it 1.87 r_mcbond_other 1.665 r_mcbond_it 1.664 r_angle_refined_deg 1.15 r_angle_other_deg 0.714
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.422 r_dihedral_angle_4_deg 17.052 r_dihedral_angle_3_deg 14.197 r_dihedral_angle_1_deg 4.808 r_mcangle_it 2.65 r_scbond_it 1.87 r_mcbond_other 1.665 r_mcbond_it 1.664 r_angle_refined_deg 1.15 r_angle_other_deg 0.714 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 1611 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing