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Crystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library, in complex with glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other the 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 3.48 64.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.604 α = 90 b = 97.604 β = 90 c = 96.241 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 1.92 50 96 0.152 0.16 12.81 10.7 75371 -3 37.178
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 1.92 2.03 83.4 1.816
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 the native structure of XEG5A 1.92 48.85 71581 3799 95.94 0.1806 0.1788 0.1784 0.2164 0.213 RANDOM 29.653
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] 0.08 0.08 0.08 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.435 r_dihedral_angle_4_deg 15.171 r_dihedral_angle_3_deg 12.674 r_dihedral_angle_1_deg 6.439 r_mcangle_it 2.879 r_mcbond_it 2.402 r_mcbond_other 2.387 r_angle_refined_deg 1.788 r_angle_other_deg 0.866 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.435 r_dihedral_angle_4_deg 15.171 r_dihedral_angle_3_deg 12.674 r_dihedral_angle_1_deg 6.439 r_mcangle_it 2.879 r_mcbond_it 2.402 r_mcbond_other 2.387 r_angle_refined_deg 1.788 r_angle_other_deg 0.866 r_chiral_restr 0.111 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 418 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data scaling PDB_EXTRACT data extraction MOLREP phasing XSCALE data scaling