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Crystal structure of triple mutant X11P(P71T+N13F+Q34L) xylanase from a metagenome derived gene from sugarcane bagasse collection site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8X65
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.6 298 0.1 M Sodium citrate buffer pH 5.6 and 35% v/v tert-Butanol
Crystal Properties Matthews coefficient Solvent content 3.3 62.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.689 α = 90 b = 105.689 β = 90 c = 70.165 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 CMOS BRUKER PHOTON 100 2023-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 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 2.3 24.64 99.7 0.128 0.139 0.053 0.996 11.7 6.6 38842 21.5
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 2.3 2.38 99.9 0.621 0.673 0.256 0.869 3.4 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.3 24.64 34152 1832 92.36 0.195 0.1924 0.1969 0.2428 0.2437 RANDOM 24.698
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] 0.8 0.4 0.8 -2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.958 r_dihedral_angle_4_deg 15.747 r_dihedral_angle_3_deg 14.322 r_dihedral_angle_1_deg 8.28 r_angle_refined_deg 1.463 r_angle_other_deg 1.298 r_chiral_restr 0.057 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.958 r_dihedral_angle_4_deg 15.747 r_dihedral_angle_3_deg 14.322 r_dihedral_angle_1_deg 8.28 r_angle_refined_deg 1.463 r_angle_other_deg 1.298 r_chiral_restr 0.057 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4523 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 6
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data reduction PHASER phasing