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Ancestral myoglobin aMbWp of Pakicetus relative
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 8 291 3.5 M ammonium sulfate solution for a 0.5 mL reservoir, and a mixture of 2 uL of the reservoir solution and 2 uL of protein solution in a 50 mM Tris-HCl (pH 8.0) buffer containing 2% (w/v) aMbWp
Crystal Properties Matthews coefficient Solvent content 2.59 52.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.39 α = 90 b = 29.74 β = 112.65 c = 58.36 γ = 90
Symmetry Space Group P 1 21 1
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 2.4 23.631 99.9 0.066 22.9 6.6 7124
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 2.4 2.53 100 0.088 21.3 6
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 2.4 23.631 1.34 7054 332 99.09 0.1862 0.1842 0.1892 0.2267 0.2307
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 22.231 f_angle_d 1.554 f_chiral_restr 0.075 f_bond_d 0.015 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1208 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction SCALA data scaling PHENIX phasing