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Glycation restrains allosteric transition in hemoglobin: The molecular basis of oxidative stress under hyperglycemic conditions in diabetes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HHO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.54 51.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 237.987 α = 90 b = 59.267 β = 125.36 c = 137.024 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD MAR CCD 165 mm 2003-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.954 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 112.13 87 23.7 3.1 69814
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 2.3 3.36 55.1 0.386
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 1HHO 2.3 112.13 57698 3020 86.97 0.2053 0.2033 0.2583 0.2443 0.2868 RANDOM 109.574
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] -0.62 -1.21 3.33 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.443 r_dihedral_angle_4_deg 17.129 r_dihedral_angle_3_deg 15.779 r_dihedral_angle_1_deg 5.876 r_angle_other_deg 3.85 r_mcangle_it 2.871 r_angle_refined_deg 1.948 r_mcbond_it 1.806 r_mcbond_other 1.799 r_chiral_restr 0.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.443 r_dihedral_angle_4_deg 17.129 r_dihedral_angle_3_deg 15.779 r_dihedral_angle_1_deg 5.876 r_angle_other_deg 3.85 r_mcangle_it 2.871 r_angle_refined_deg 1.948 r_mcbond_it 1.806 r_mcbond_other 1.799 r_chiral_restr 0.142 r_gen_planes_other 0.039 r_bond_refined_d 0.019 r_gen_planes_refined 0.013 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10886 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 491
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling AMoRE phasing