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Biochemical implications of the substitution of a unique cysteine residue in sugar beet phytoglobin BvPgb 1.2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZHW 3zhw.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293.15 0.1 M MIB (Sodium malonate dibasic monohydrate, Imidazole, Boric acid) pH 8.0, 25 % (w/v) PEG 1500.
Crystal Properties Matthews coefficient Solvent content 2.15 42.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.85 α = 90 b = 73.92 β = 105.05 c = 62.83 γ = 90
Symmetry Space Group P 1 21 1
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 2020-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97996 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.242 60.675 99.9 0.072 0.999 12.7 7 15684 54.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.242 2.281 100 0.874 0.953 7.1
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 3zhw.pdb 2.24 35.59 1.36 15558 797 99.08 0.264 0.2625 0.2655 0.2881 0.2942 105.62
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 13.7165 f_angle_d 0.5344 f_chiral_restr 0.0358 f_plane_restr 0.0032 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2293 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 86
Software Software Software Name Purpose MxCuBE data collection autoPROC data processing XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement