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X-ray crystal structure of VioC bound to Fe(II), 3S-hydroxy-L-homoarginine, and succinate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8.5 293 2-oxoglutarate, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.17 43.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.788 α = 90 b = 66.388 β = 109.6 c = 63.042 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 CCD RAYONIX MX-300 2016-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.979 APS 21-ID-F
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 1.95 59.39 98.4 0.076 0.088 0.045 7.2 3.8 22782
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 1.95 1.98 97.5 0.448 0.52 0.264 0.894 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.94 59.39 21514 1105 96.28 0.2026 0.2007 0.209 0.2391 0.2434 RANDOM 22.166
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] 0.34 -0.2 -0.3 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.845 r_dihedral_angle_4_deg 16.376 r_dihedral_angle_3_deg 12.257 r_dihedral_angle_1_deg 5.351 r_angle_refined_deg 1.014 r_angle_other_deg 0.731 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.845 r_dihedral_angle_4_deg 16.376 r_dihedral_angle_3_deg 12.257 r_dihedral_angle_1_deg 5.351 r_angle_refined_deg 1.014 r_angle_other_deg 0.731 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2630 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing