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IscU D40A variant from Methanothrix thermoacetophila
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7C8N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2M Calcium acetate, 0.1M Tris pH 7.0, 20% w/v PEG3000
Crystal Properties Matthews coefficient Solvent content 1.77 39.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.49 α = 90 b = 40.28 β = 100.91 c = 90.24 γ = 90
Symmetry Space Group P 1 21 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 2023-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
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 1.8 50 99.57 0.07731 0.09184 0.04913 0.996 7.85 3.4 39984 26.9
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 1.8 1.85 99.8 0.7572 0.895 0.4731 0.799 2.31 3.5
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 1.8 39.25 1.37 39888 1997 99.57 0.1978 0.1964 0.1964 0.2237 0.2238 32.57
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 13.0575 f_angle_d 1.1531 f_chiral_restr 0.0693 f_bond_d 0.0109 f_plane_restr 0.0093
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3733 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling MOLREP phasing