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X-ray crystal structure of His-tagged Y140F FtmOx1 bound to Fe(II) and 2-oxoglutarate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZON PDB entry 4ZON
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8.5 293 PEG4000, magnesium chloride, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.07 35.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.512 α = 90 b = 79.362 β = 90 c = 91.511 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 2017-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.979 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 1.92 50 98.8 0.08 0.087 0.033 7.9 6.7 40810
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 1.92 1.95 93.7 0.85 0.93 0.371 0.833 5.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4ZON 1.92 59.96 33672 1679 85.61 0.2313 0.23 0.2584 0.2566 RANDOM 25.527
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] -0.45 1.02 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.9 r_dihedral_angle_4_deg 15.326 r_dihedral_angle_3_deg 13.824 r_dihedral_angle_1_deg 6.096 r_angle_refined_deg 1.033 r_angle_other_deg 0.739 r_chiral_restr 0.062 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.9 r_dihedral_angle_4_deg 15.326 r_dihedral_angle_3_deg 13.824 r_dihedral_angle_1_deg 6.096 r_angle_refined_deg 1.033 r_angle_other_deg 0.739 r_chiral_restr 0.062 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4533 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 22
Software Software Software Name Purpose HKL-2000 data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing