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DtxR-like iron-dependent regulator IdeR (P39G variant) 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 3.69 66.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.395 α = 90 b = 113.841 β = 117.25 c = 89.795 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 2.05 54.93 93.1 0.082 0.088 0.033 0.998 12 7 76685
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 2.05 2.23 61.6 1.305 1.411 0.532 0.573 1.7 6.9
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 2.05 54.93 72891 3794 70.14 0.2273 0.2257 0.2326 0.2589 0.2649 RANDOM 51.319
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] 0.01 -0.05 -0.06 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.756 r_dihedral_angle_4_deg 14.622 r_dihedral_angle_3_deg 12.139 r_dihedral_angle_1_deg 4.784 r_angle_refined_deg 1.099 r_angle_other_deg 1.094 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 25.756 r_dihedral_angle_4_deg 14.622 r_dihedral_angle_3_deg 12.139 r_dihedral_angle_1_deg 4.784 r_angle_refined_deg 1.099 r_angle_other_deg 1.094 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 6921 Nucleic Acid Atoms 1189 Solvent Atoms 192 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing