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Old Yellow Enzyme from the thermophilic Ferrovum sp. JA12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 Lanthanides mix (0.0005M Yttrium(III) chloride hexahydrate, 0.0005M Erbium(III) chloride hexahydrate, 0.0005M Terbium(III) chloride hexahydrate, 0.0005M Ytterbium(III) chloride hexahydrate), MOPSO, Bis-Tris,
PEG 20000, Trimethylolpropane, NDSB 195
Crystal Properties Matthews coefficient Solvent content 3.62 66.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.712 α = 90 b = 187.712 β = 90 c = 129.317 γ = 90
Symmetry Space Group P 41 2 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 PILATUS 6M 2020-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97856 ESRF ID30B
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 2.3 48.3 99.43 0.998 17.09 12.9 102408 35.09
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 2.3 2.382 0.977
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 2.3 48.3 1.33 101862 5135 99.45 0.1811 0.1798 0.1836 0.205 0.2093 39.66
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 21.7892 f_angle_d 0.5777 f_chiral_restr 0.0457 f_plane_restr 0.004 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10940 Nucleic Acid Atoms Solvent Atoms 642 Heterogen Atoms 214
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing