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Neutron Structure of Compound II of Ascorbate Peroxidase
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 300 2.25 M Lithium sulfate, 0.1 M HEPES pH 8.3 - 8.9
Crystal Properties Matthews coefficient Solvent content 2.23 44.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.095 α = 90 b = 82.095 β = 90 c = 75.162 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 neutron 100 IMAGE PLATE MAATEL IMAGINE multilayer 2015-10-14 L LAUE 2 1 x-ray 100 CCD RIGAKU SATURN 944+ multilayer 2015-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 NUCLEAR REACTOR ILL BEAMLINE LADI III 3.2 - 4.2 ILL LADI III 2 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 2.2 40 69.8 0.18 7 4 9220 2 1.8 19.91 98.72 0.16 9.4 6.8 23857
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.806 19.91 1.36 23857 1194 98.72 0.1578 0.1547 0.1513 0.2159 0.2129 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.202 36.714 2.03 9220 462 68.14 0.2401 0.2364 0.3104
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] 0.4889 0.4889 -0.9778 0.4889 0.4889 -0.9778
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.898 f_dihedral_angle_d 11.898 f_angle_d 1.366 f_angle_d 1.366 f_chiral_restr 0.115 f_chiral_restr 0.115 f_bond_d 0.016 f_bond_d 0.016 f_plane_restr 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1899 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing