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Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 13% oxygen saturation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 11-12 % (w/v) polyethylene glycol (PEG) 10,000, 10 mM CaCl2, 200 mM Tris-HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.64 53.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.925 α = 90 b = 110.925 β = 90 c = 271.047 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS EIGER X 4M 2017-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.100 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 2.1 50 99.8 0.178 0.997 11 10.1 37707 30.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.23 1.56 0.779 1.7
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 2ZFO 2.1 47.3 1.35 37668 1873 99.67 0.1831 0.1812 0.1814 0.2202 0.2192 36.53
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 14.8885 f_angle_d 0.7059 f_chiral_restr 0.0348 f_bond_d 0.0033 f_plane_restr 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4257 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 180
Software Software Software Name Purpose PHENIX refinement PHASER phasing XDS data reduction XDS data scaling