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Crystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from metagenomic library, in complex with a xyloglucan oligosaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other native structure of XEG5A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 PEG3350, PEG400, magnesium chloride
Crystal Properties Matthews coefficient Solvent content 3.38 63.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.504 α = 90 b = 96.504 β = 90 c = 95.857 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2014-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.459 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.15 50 97.6 0.2 0.223 7.72 5.3 53072 -3 36.459
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.28 96.1 1.35
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 MOLECULAR REPLACEMENT THROUGHOUT native structure of XEG5A 2.15 43.14 50382 2696 97.63 0.1903 0.1879 0.1837 0.2338 0.2263 RANDOM 30.885
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] 0.2 0.2 0.2 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.13 r_dihedral_angle_4_deg 17.712 r_dihedral_angle_3_deg 14.127 r_dihedral_angle_1_deg 6.268 r_mcangle_it 3.072 r_mcbond_it 2.271 r_mcbond_other 2.267 r_angle_refined_deg 1.776 r_angle_other_deg 0.858 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.13 r_dihedral_angle_4_deg 17.712 r_dihedral_angle_3_deg 14.127 r_dihedral_angle_1_deg 6.268 r_mcangle_it 3.072 r_mcbond_it 2.271 r_mcbond_other 2.267 r_angle_refined_deg 1.776 r_angle_other_deg 0.858 r_chiral_restr 0.097 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5374 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data scaling PDB_EXTRACT data extraction MOLREP phasing XSCALE data scaling