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Class 1 Phytoglobin from Sugar beet (BvPgb1.2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZHW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 20% (w/v) PEG6000, 0.1 M Citrate, pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.91 57.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.75 α = 90 b = 96.75 β = 90 c = 47.9 γ = 90
Symmetry Space Group P 4 21 2
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 2019-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9537 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 68.413 100 0.999 23.7 25.6 18443 38.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.901 1.934 0.727
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 1.9 47.9 1.36 18440 969 99.97 0.2038 0.2027 0.2063 0.2353 0.2367 42.94
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 5.9939 f_angle_d 1.4649 f_chiral_restr 0.0566 f_bond_d 0.0105 f_plane_restr 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1145 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 58
Software Software Software Name Purpose MxCuBE data collection autoPROC data processing XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement