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Crystal structure of liganded Hb with the 5-HMF analog, MMA509
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IC0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 30 mg/dL of CO-ligated Hb crystallized using 10-20% PEG 6000, 100 mM Hepes, pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.1 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.758 α = 90 b = 83.652 β = 90 c = 105.235 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 PIXEL DECTRIS EIGER R 4M VariMax TM-VHF Arc)Sec Confocal Optical System 2020-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 28.3 100 0.067 0.072 0.026 0.999 24.8 7.4 38189 20.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99.9 0.42 0.455 0.171 0.932 6.9
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 THROUGHOUT 3IC0 2 28.298 1.33 38096 1879 99.88 0.1707 0.1672 0.1688 0.2393 0.2397 21.6014
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 13.687 f_angle_d 0.891 f_chiral_restr 0.049 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4384 Nucleic Acid Atoms Solvent Atoms 765 Heterogen Atoms 204
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction CrysalisPro data reduction PHASER phasing