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Crystal structure of native xylose isomerase from Piromyces E2 grown in yeast, in complex with xylose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NH5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 14-17 % PEG3350, HEPES, pH 7
Crystal Properties Matthews coefficient Solvent content 2.3 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.454 α = 115.46 b = 79.267 β = 89.99 c = 91.878 γ = 117.07
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MARRESEARCH 2018-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.86 46.6 93.6 0.066 0.09 0.06 0.931 7.1 2.1 135735
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.89 79.1 0.38 0.518 0.35 0.286 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT 5NH5 1.86 46.6 128946 6788 93.61 0.1405 0.1386 0.149 0.1763 0.1847 RANDOM 18.438
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] 1.1 0.55 -0.11 -0.28 -0.36 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.68 r_dihedral_angle_4_deg 15.947 r_dihedral_angle_3_deg 14.367 r_dihedral_angle_1_deg 6.681 r_angle_refined_deg 1.55 r_angle_other_deg 1.443 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.68 r_dihedral_angle_4_deg 15.947 r_dihedral_angle_3_deg 14.367 r_dihedral_angle_1_deg 6.681 r_angle_refined_deg 1.55 r_angle_other_deg 1.443 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13876 Nucleic Acid Atoms Solvent Atoms 1907 Heterogen Atoms 263
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing