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Crystal structure of Manganese-rebound N(omega)-hydroxy-L-arginine hydrolase with oxidized Cys86
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LUH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 298 PEG 4000, MgCl2
Crystal Properties Matthews coefficient Solvent content 1.96 37.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.94 α = 85.33 b = 46.743 β = 86.91 c = 58.338 γ = 70.59
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2022-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.26 43.99 89.9 0.055 0.073 0.047 0.995 6.1 2 110843
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 1.26 1.28 49.7 0.548 0.734 0.485 0.538 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.26 35.22 1.95 110835 5468 89.94 0.1658 0.1648 0.1653 0.1862 0.1869
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.727 f_angle_d 0.863 f_chiral_restr 0.082 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4057 Nucleic Acid Atoms Solvent Atoms 582 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHENIX phasing