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Crystal Structure of the MetH Reactivation Domain bound to Sinefungin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MSK pdbid 1MSK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 293 28% PEG 6000, 100mM Tris pH 7.3, 300mM magnesium acetate:15mg/mL protein, 3mM sinefungin, 10mM Tris 7.2, 10mM EDTA, 2:2uL
Crystal Properties Matthews coefficient Solvent content 2.18 43.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.35 α = 90 b = 61.577 β = 90 c = 139.877 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2016-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.5 50 98.5 0.061 0.067 0.027 13.7 5.9 51658 15.52
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 1.5 1.53 87.7 0.28 0.315 0.14 0.959 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT pdbid 1MSK 1.512 32.553 1.37 51571 2579 97.75 0.1458 0.1437 0.1444 0.1859 0.1858 24.2995
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 3.321 f_angle_d 1.042 f_chiral_restr 0.063 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2563 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 27
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction