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X-ray structure analysis of xylanase-N44E with MES at pH6.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DFB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 16% PEG8000, 0.2 M NaI, 0.1 M MES-NaOH at pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.4 48.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.99 α = 90 b = 59.627 β = 90 c = 69.552 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 100 IMAGE PLATE RIGAKU RAXIS IV++ Mirrors 2013-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.5 50 96.5 0.066 17 3.8 31754
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 92.7 0.427 3.1 3.8
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2DFB 1.5 32.93 1.34 31711 1602 96.1 0.1744 0.1742 0.1756 0.1786 0.1814 random selection 19.5
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 13.077 f_angle_d 1.191 f_chiral_restr 0.084 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1473 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 17
Software Software Software Name Purpose DENZO data reduction PHENIX refinement PDB_EXTRACT data extraction SCALEPACK data scaling PHASER phasing