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Structure of turkey hemoglobin A covalently bound with epigallocatechin gallate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K8B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 THE CONCENTRATION OF HB-EGCG ADDUCT WAS 16 MG/ML IN 10 MM TRIS PH 8.0. THE CRYSTALLIZATION RESERVOIR WAS 20% PEG3350, 0.1 M RACEMIC MALIC ACID, 0.05 M HEPES PH 7.0. 200 NL PROTEIN + 150 NL RESERVOIR. SET BY MOSQUITO IN MRC SD2 PLATES, 50 MICROLITER RESERVOIRS
Crystal Properties Matthews coefficient Solvent content 2.36 47.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80 α = 90 b = 81.6 β = 90 c = 90.52 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 X 16M 2017-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033202 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.995 48.31 99.9 0.192 0.2 0.998 8.84 13.2 40813
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 2.303 2.394 0.811
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.995 39.58 1.34 40813 2014 99.44 0.1985 0.1963 0.1969 0.2391 0.2398 47.11
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 11.4296 f_angle_d 0.8455 f_chiral_restr 0.044 f_plane_restr 0.0086 f_bond_d 0.0082
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4408 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 243
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling XDS data reduction PDB_EXTRACT data extraction PHASER phasing