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Crystal structure of VioC in complex with Fe(II), (2S,3S)- hydroxyarginine, and succinate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OG5 PDB ENTRY 2OG5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 1.0 M NA-SUCCINATE, 0.1 M TRIS/HCL PH 8.0, 3 MM (2S\,3S)-HYDROXYARGININE
Crystal Properties Matthews coefficient Solvent content 2.03 39.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.77 α = 90 b = 66.93 β = 109.16 c = 62.9 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 MARRESEARCH MIRRORS 2008-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.16 20 91.3 0.06 10.6 3 99570 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.16 1.19 51.1 0.25 2.1
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 PDB ENTRY 2OG5 1.16 19.96 97778 1791 91.3 0.13293 0.13224 0.1471 0.17099 0.1804 RANDOM 13.984
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] 0.09 -0.61 -0.32 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.726 r_sphericity_free 21.528 r_dihedral_angle_4_deg 18.264 r_dihedral_angle_3_deg 13.705 r_scangle_it 9.548 r_sphericity_bonded 8.402 r_scbond_it 7.79 r_dihedral_angle_1_deg 7.198 r_mcangle_it 6.612 r_mcbond_it 5.537
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.726 r_sphericity_free 21.528 r_dihedral_angle_4_deg 18.264 r_dihedral_angle_3_deg 13.705 r_scangle_it 9.548 r_sphericity_bonded 8.402 r_scbond_it 7.79 r_dihedral_angle_1_deg 7.198 r_mcangle_it 6.612 r_mcbond_it 5.537 r_rigid_bond_restr 4.69 r_mcbond_other 2.996 r_angle_refined_deg 1.355 r_angle_other_deg 0.809 r_symmetry_vdw_other 0.398 r_symmetry_vdw_refined 0.262 r_nbd_other 0.24 r_xyhbond_nbd_refined 0.228 r_nbd_refined 0.224 r_symmetry_hbond_refined 0.223 r_nbtor_refined 0.179 r_chiral_restr 0.089 r_nbtor_other 0.087 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_gen_planes_other 0.004 r_bond_other_d 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2595 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing