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VioC L-arginine hydroxylase bound to Fe(II), L-arginine, and 2-OXO-GLUTARIC ACID
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1 M 2-oxoglutarate, 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 1.84 33.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.336 α = 90 b = 66.99 β = 108.81 c = 62.665 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 225 mm CCD 2014-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 1.0 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 1.6 50 97.4 0.053 0.057 0.02 8.1 7.7 40551
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 1.6 1.63 92.5 0.657 0.705 0.255 0.91 7.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2WBO 1.6 50 38492 2050 97.27 0.1993 0.1977 0.2103 0.2311 0.2409 RANDOM 20.377
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] 1.15 -2.09 -0.09 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.71 r_dihedral_angle_4_deg 13.046 r_dihedral_angle_3_deg 11.314 r_dihedral_angle_1_deg 5.208 r_angle_refined_deg 0.947 r_angle_other_deg 0.692 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.71 r_dihedral_angle_4_deg 13.046 r_dihedral_angle_3_deg 11.314 r_dihedral_angle_1_deg 5.208 r_angle_refined_deg 0.947 r_angle_other_deg 0.692 r_chiral_restr 0.052 r_bond_refined_d 0.004 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 2647 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 23
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing