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Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S variant with trans heme D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TT9 Apo chain A, F34Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.1 M Bis-Tris pH 5.5, 25% PEG MME 2000, 10 mM KCN, 18 days in the dark, 43 days exposed to laboratory ambient light
Crystal Properties Matthews coefficient Solvent content 2.07 40.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.357 α = 90 b = 104.809 β = 90 c = 150.551 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 110 PIXEL RIGAKU HyPix-6000HE 2023-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU PhotonJet-R 1.54184
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 1.8 24.25 99.5 0.032 54.01 6.8 41341
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 1.8 1.87 99.8 0.278 3.97 4.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 24.25 0.15 40960 1982 98.84 0.1999 0.1981 0.2359 0.211
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 12.022 f_angle_d 0.659 f_chiral_restr 0.041 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3592 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 348
Software Software Software Name Purpose PHENIX refinement CrysalisPro data scaling CrysalisPro data reduction PHASER phasing