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Neutron structure of ferric ascorbate peroxidase
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JPR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 300 Lithium Sulfate
HEPES
Crystal Properties Matthews coefficient Solvent content 2.3 46.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.904 α = 90 b = 82.904 β = 90 c = 75.868 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 2017-10-01 L LAUE 2 1 x-ray 100 CCD RIGAKU SATURN 944+ 2017-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 NUCLEAR REACTOR ILL BEAMLINE LADI III 2.87-3.4 ILL LADI III 2 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 36.68 77.5 0.1 5.9 3.3 10136 2 1.9 20.11 99.9 0.1 11.1 11.2 21444
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 0.2 2 1.9 1.94 0.7
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 1.9 20.107 1.36 21404 1071 99.99 0.1467 0.1445 0.1885 31.17 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.222 37.076 1.79 10135 508 74.75 0.278 0.2763 0.3076
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] -3.7555 -3.7555 -5.7725 -3.7555 -3.7555 -5.7725
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.938 f_angle_d 1.521 f_chiral_restr 0.092 f_bond_d 0.013 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1905 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 78
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction