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X-ray crystal structure of VioC bound to Fe(II), D-arginine, and 2-oxoglutarate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8.5 293 2-oxoglutarate, TRIS-HCl
Crystal Properties Matthews coefficient Solvent content 2.11 41.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.957 α = 90 b = 67.039 β = 108.15 c = 62.13 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 MARMOSAIC 300 mm CCD 2015-02-15 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 1.9 59.04 93.7 0.066 0.078 0.04 8.6 3.7 23222
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 1.9 1.93 85.4 0.491 0.577 0.3 0.878 3.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.89 59.04 22004 1196 92.66 0.222 0.2201 0.2562 0.2575 RANDOM 27.716
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] -1.33 -3.55 -0.12 3.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.058 r_dihedral_angle_4_deg 12.746 r_dihedral_angle_3_deg 12.312 r_dihedral_angle_1_deg 5.282 r_angle_refined_deg 0.993 r_angle_other_deg 0.707 r_chiral_restr 0.055 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 33.058 r_dihedral_angle_4_deg 12.746 r_dihedral_angle_3_deg 12.312 r_dihedral_angle_1_deg 5.282 r_angle_refined_deg 0.993 r_angle_other_deg 0.707 r_chiral_restr 0.055 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 2415 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 23
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing