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Crystal Structures of Mutant Endo-beta-1,4-xylanase II (Y88F)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DFC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6 291 20% PEG 8000, 0.2M NaI, 0.1M MES
Crystal Properties Matthews coefficient Solvent content 2.42 49.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.331 α = 90 b = 59.327 β = 90 c = 70.056 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 80 CCD ADSC QUANTUM 315r 2017-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 1.0 SSRF BL19U1
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 1.15 39.782 98.15 0.03235 0.994 19.45 5.7 70926 8.82
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 1.15 1.191 87.23 0.1112 0.951 6.35 5.8
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 THROUGHOUT 2DFC 1.15 39.782 1.38 70852 3587 98.16 0.1376 0.137 0.1416 0.1483 0.1495 12.3019
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 12.825 f_angle_d 1.113 f_chiral_restr 0.101 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1471 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALEPACK data scaling PDB_EXTRACT data extraction PHASER phasing