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Quiescin Sulfhydryl Oxidase from Rattus norvegicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1 M sodium citrate buffer, pH 6.0, 0.25 M NaCl, 27% w/v polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.41 50.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.495 α = 90 b = 169.583 β = 90 c = 68.369 γ = 90
Symmetry Space Group P 21 21 2
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 2012-06-21 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 48.78 99.89 0.149 10.6 4.6 25595 33
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 2.9 2.96 99.9 0.357 2.7 4.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3T58 2.9 48.78 1.37 25589 1759 99.9 0.182 0.178 0.1823 0.243 0.244 Random selection 28
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 11.533 f_angle_d 0.686 f_chiral_restr 0.046 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7875 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 106
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling PHASER phasing CNS refinement DENZO data reduction