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R2-like ligand-binding oxidase with aerobically reconstituted Mn/Fe cofactor (long soak)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HR0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 22.5% (w/v) PEG 1500, 0.1 M HEPES-Na pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.39 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.058 α = 90 b = 97.419 β = 90 c = 129.32 γ = 90
Symmetry Space Group I 2 2 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 PIXEL DECTRIS PILATUS 6M 2012-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.006 50 99.3 0.155 5.35 3.7 23996 -3 37.8
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 2.006 2.13 99.2 0.409 1.7 3.8
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 4HR0 2.006 38.906 2.09 23992 1197 99.34 0.1716 0.1692 0.1733 0.2165 0.2173 random selection 49.1
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 15.757 f_angle_d 1.216 f_chiral_restr 0.057 f_bond_d 0.017 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2377 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling Coot model building PHASER phasing