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Crystal structure of as-isolated Fe(III)Fe(III) Streptomyces griseoflavus HrmI in complex with L-lysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Experimentally phased model using SeMet incorporation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 0.1 M Tris pH 7.0, 0.2 M MgCl2, 15% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.37 48.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.128 α = 90 b = 74.553 β = 103.174 c = 51.23 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 EIGER2 XE 16M KB mirrors 2023-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.979497 SSRL BL12-1
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 1.7 37.28 96.18 0.08108 0.0875 0.03261 0.999 15.69 7.1 41229 22.53
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 1.7 1.761 1.072 1.156 0.4279 0.669 1.57
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.7 37.28 1.34 41229 2000 95.89 0.1745 0.1733 0.1738 0.1981 0.1979 25.72
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.9378 f_angle_d 1.1789 f_chiral_restr 0.0751 f_bond_d 0.0129 f_plane_restr 0.0115
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2709 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement PHENIX phasing XDS data reduction XDS data scaling