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Oxidoreductase Fragment of Mouse QSOX1 in Complex with a FAb Fragment from an Antibody Targeting Mouse and Human QSOX1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D8I 5D8I, 4IJ3 experimental model PDB 4IJ3 5D8I, 4IJ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 50 mM CaCl2, 0.1 M 2-(N-morpholino)ethanesulfonic acid buffer, pH 6, 22.5% w/v PEG 6 kD
Crystal Properties Matthews coefficient Solvent content 2.44 49.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.799 α = 90 b = 204.77 β = 90 c = 44.669 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU RAXIS IV++ 2015-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.3 50 99.7 0.084 0.084 8.3 3.1 62461 -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 2.3 2.34 100 0.418 2.2 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5D8I, 4IJ3 2.3 27.424 1.37 62422 2002 99.68 0.1704 0.1672 0.2279 0.2112 random selection 34.98
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 13.909 f_angle_d 1.014 f_chiral_restr 0.036 f_plane_restr 0.006 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10170 Nucleic Acid Atoms Solvent Atoms 425 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling PHASER phasing