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DtxR-like iron-dependent regulator IdeR complexed with cobalt and its consensus DNA-binding sequence
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7B1V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 30%(w/v) PEG 2000 MME, 0.2 M ammonium sulfate, 0.1 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 3.58 65.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 195.035 α = 90 b = 112.899 β = 117.07 c = 88.505 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2020-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97624 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.12 78.94 92.5 0.092 0.099 0.038 0.997 11.2 6.9 60545
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.32 59 1.203 1.304 0.497 0.581 1.7 6.7
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 7B1V 2.12 78.94 57538 3007 62.77 0.2308 0.2297 0.2326 0.2526 0.2564 RANDOM 50.015
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] 0.12 0.07 0.15 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.334 r_dihedral_angle_4_deg 16.038 r_dihedral_angle_3_deg 12.691 r_dihedral_angle_1_deg 4.95 r_angle_refined_deg 1.1 r_angle_other_deg 1.078 r_chiral_restr 0.038 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.334 r_dihedral_angle_4_deg 16.038 r_dihedral_angle_3_deg 12.691 r_dihedral_angle_1_deg 4.95 r_angle_refined_deg 1.1 r_angle_other_deg 1.078 r_chiral_restr 0.038 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7002 Nucleic Acid Atoms 1189 Solvent Atoms 136 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing