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Crystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from metagenomic library, in complex with cellotriose
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 3.39 63.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.704 α = 90 b = 96.704 β = 90 c = 95.719 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 2.4 50 97.9 0.191 0.211 10.01 5.5 38307 -3 47.973
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 2.4 2.55 96.4 1.425
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT native structure of XEG5A 2.4 43.2 36412 1922 97.97 0.2222 0.2204 0.2562 0.2034 RANDOM 40.001
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] 0.64 0.64 0.64 -2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.016 r_dihedral_angle_4_deg 13.855 r_dihedral_angle_3_deg 13.051 r_dihedral_angle_1_deg 5.296 r_mcangle_it 1.729 r_mcbond_it 1.04 r_mcbond_other 1.04 r_angle_refined_deg 0.947 r_angle_other_deg 0.678 r_chiral_restr 0.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.016 r_dihedral_angle_4_deg 13.855 r_dihedral_angle_3_deg 13.051 r_dihedral_angle_1_deg 5.296 r_mcangle_it 1.729 r_mcbond_it 1.04 r_mcbond_other 1.04 r_angle_refined_deg 0.947 r_angle_other_deg 0.678 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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 93 Heterogen Atoms 70
Software Software Software Name Purpose XDS data scaling REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling