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Xylose Isomerase in 70% relative humidity environment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RNF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 35% (w/v) PEG3350, 200 mM lithium sulfate and 10 mM Hepes/NaOH, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.25 45.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.826 α = 90 b = 96.307 β = 90 c = 97.757 γ = 90
Symmetry Space Group P 21 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 293 PIXEL DECTRIS EIGER2 X 16M 2022-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
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 1.63 52.83 61.88 0.088 0.999 11.9 6.2 60298 16.69
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 1.63 1.69 1.6 0.593
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 6RNF 1.63 52.83 1.34 60293 3036 61.88 0.1615 0.1598 0.1597 0.1937 0.1939 20.95
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 5.4122 f_angle_d 1.0543 f_chiral_restr 0.0535 f_plane_restr 0.0119 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6092 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing