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Ancestral myoglobin aMbWb' of Basilosaurus relative (polyphyly)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YCJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 291 0.1 M MIB buffer (25 mM sodium malonate dibasic monohydrate, 37.5 mM boric acid, 37.5 mM imidazole pH 9.0), 25 % (w/v) PEG1500, 2% (w/v) aMbWb'
Crystal Properties Matthews coefficient Solvent content 2.12 42.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.29 α = 90 b = 69.32 β = 90 c = 108.13 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 x-ray 100 CCD RAYONIX MX225-HS 2015-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0000 SPring-8 BL26B2
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 1.97 25 99.9 0.058 38.8 12.3 21695
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 1.97 2.07 99.8 0.087 33.6 10.1
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5YCJ 1.97 24.983 1.34 21421 1099 99.22 0.1735 0.1712 0.1782 0.2165 0.2215
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 25.405 f_angle_d 1.292 f_chiral_restr 0.398 f_bond_d 0.013 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2444 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 86
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction SCALA data scaling PHENIX phasing