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Joint neutron/X-ray structure of Oxyferrous Dehaloperoxidase B
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V5J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 277 2000 MPEG, ammonium sulfate, cacodylate
Crystal Properties Matthews coefficient Solvent content 2.29 46.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.83 α = 90 b = 67.1 β = 90 c = 69.04 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 neutron 298 IMAGE PLATE MAATEL IMAGINE 2017-02-24 L LAUE 2 1 x-ray 298 IMAGE PLATE RIGAKU RAXIS IV++ 2017-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 NUCLEAR REACTOR ORNL High Flux Isotope Reactor BEAMLINE CG4D 2.8-4.6 ORNL High Flux Isotope Reactor CG4D 2 SEALED TUBE RIGAKU MICROMAX-007 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 17.48 79.3 0.106 4.7 5.5 11267 2 1.95 48.13 99.5 0.022 0.022 0.999 26.8 2 21117
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 2.32 0.201 2.2 2 1.95 2.02 0.135 0.191 0.135 0.938 1.9
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 2.2 17.435 1.38 14803 1480 99.72 0.1604 0.1546 0.1555 0.2123 0.2126 35.3425 NEUTRON DIFFRACTION 2.215 17.484 11263 1127 77.44 0.2548 0.2491 0.3049
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2112 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 158
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing SCALA data scaling LAUEGEN data reduction