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Crystal structure of GH115 enzyme AxyAgu115A from Amphibacillus xylanus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZMH 4ZMH, 4C90 experimental model PDB 4C90 4ZMH, 4C90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 20 mg/mL protein solution with 0.5 microL of reservoir solution 20% (w/v) PEG 3350, 0.2 M diammonium hydrogen citrate and 10 mM D-glucuronic acid
Crystal Properties Matthews coefficient Solvent content 2.99 58.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.08 α = 84.37 b = 96.21 β = 78.37 c = 111.75 γ = 83.32
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2018-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97913 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.99 47.64 94.6 0.102 0.042 0.999 14.1 11.9 165501
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.04 90.8 0.534 0.534 0.82 3.9 3.9
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 4ZMH, 4C90 1.99 47.638 1.96 165435 8156 94.62 0.1496 0.1475 0.1486 0.1896 0.1903 RANDOM
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 20.518 f_angle_d 1.133 f_chiral_restr 0.075 f_bond_d 0.012 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15470 Nucleic Acid Atoms Solvent Atoms 1837 Heterogen Atoms 117
Software Software Software Name Purpose PHENIX refinement X-Area data reduction Aimless data scaling PHENIX phasing PHENIX model building Coot model building