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DtxR-like iron-dependent regulator IdeR (Q43A 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 6.5 293 29%(w/v) PEG 3350, 0.28 M ammonium sulfate, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 3.44 64.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.656 α = 90 b = 110.856 β = 116.85 c = 86.752 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 2019-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97622 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 2.34 93.16 89.5 0.13 0.141 0.054 0.997 9.1 6.8 36928
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 2.34 2.63 61.1 1.218 1.323 0.511 0.599 1.8 6.5
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 7B1V 2.34 93.16 35059 1869 53.86 0.268 0.2673 0.2616 0.2831 0.2797 RANDOM 62.742
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] -0.07 -0.27 0.78 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.965 r_dihedral_angle_4_deg 16.453 r_dihedral_angle_3_deg 12.649 r_dihedral_angle_1_deg 5.163 r_angle_refined_deg 1.146 r_angle_other_deg 1.113 r_chiral_restr 0.041 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.965 r_dihedral_angle_4_deg 16.453 r_dihedral_angle_3_deg 12.649 r_dihedral_angle_1_deg 5.163 r_angle_refined_deg 1.146 r_angle_other_deg 1.113 r_chiral_restr 0.041 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7016 Nucleic Acid Atoms 1189 Solvent Atoms 43 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing