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DtxR-like iron-dependent regulator IdeR complexed with cobalt
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U8R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 25%(w/v) PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.17 43.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.888 α = 109.12 b = 45.564 β = 93.2 c = 66.275 γ = 113.98
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 EIGER2 X 16M 2019-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 2.04 61.1 83.5 0.058 0.069 0.037 0.997 10.3 3.3 17216
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 2.04 2.22 54.2 0.579 0.748 0.465 0.658 1.5 2.4
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 1U8R 2.04 61.1 16378 838 62.74 0.2335 0.232 0.2353 0.2618 0.2615 RANDOM 35.79
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] 0.27 0.17 -0.06 0.23 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.299 r_dihedral_angle_4_deg 12.278 r_dihedral_angle_3_deg 11.669 r_dihedral_angle_1_deg 4.736 r_angle_refined_deg 1.149 r_angle_other_deg 1.017 r_chiral_restr 0.033 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 28.299 r_dihedral_angle_4_deg 12.278 r_dihedral_angle_3_deg 11.669 r_dihedral_angle_1_deg 4.736 r_angle_refined_deg 1.149 r_angle_other_deg 1.017 r_chiral_restr 0.033 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 3420 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing