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Crystal structure of VioC in complex with (2S,3S)-hydroxyarginine
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 7.5 0.6 M TRI-SODIUM CITRATE 0.1 M HEPES PH 7.5 3 MM (2S,3S)-HYDROXYARGININE
Crystal Properties Matthews coefficient Solvent content 2.03 39.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.91 α = 90 b = 66.83 β = 109.17 c = 62.73 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 1.1 20 96.8 0.04 14.1 3.6 123576 -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 1.1 1.13 84.9 0.57 1.5
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 1.1 19.75 121303 2249 96.8 0.144 0.143 0.1578 0.178 0.19 RANDOM 14.18
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] -0.31 -0.98 -0.39 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.153 r_dihedral_angle_4_deg 17.46 r_scangle_it 13.345 r_dihedral_angle_3_deg 12.884 r_scbond_it 11.799 r_mcangle_it 7.913 r_mcbond_it 7.25 r_dihedral_angle_1_deg 6.786 r_angle_refined_deg 1.449 r_angle_other_deg 1.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.153 r_dihedral_angle_4_deg 17.46 r_scangle_it 13.345 r_dihedral_angle_3_deg 12.884 r_scbond_it 11.799 r_mcangle_it 7.913 r_mcbond_it 7.25 r_dihedral_angle_1_deg 6.786 r_angle_refined_deg 1.449 r_angle_other_deg 1.282 r_symmetry_vdw_other 0.417 r_symmetry_hbond_refined 0.28 r_symmetry_vdw_refined 0.255 r_nbd_other 0.253 r_xyhbond_nbd_refined 0.236 r_nbd_refined 0.229 r_nbtor_refined 0.183 r_chiral_restr 0.087 r_nbtor_other 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.002 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2594 Nucleic Acid Atoms Solvent Atoms 461 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing