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Crystal structure of X11P(P71T) 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 2VUJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 298 0.1 M MES monohydrate pH 6.5
12% w/v Polyethylene glycol 20,000
Crystal Properties Matthews coefficient Solvent content 1.92 36.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.466 α = 90 b = 68.547 β = 90 c = 74.4 γ = 90
Symmetry Space Group P 21 21 21
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 2020-07-24 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 1.7 23.73 99.5 0.044 0.049 0.02 0.999 24 5.2 19998 3.5
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 1.7 1.73 97.1 0.136 0.163 0.089 0.965 8.9 3.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.7 23.73 18678 984 97.97 0.1444 0.1433 0.1656 0.1691 RANDOM 6.053
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] 0.33 -0.36 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.462 r_dihedral_angle_4_deg 22.151 r_dihedral_angle_3_deg 10.717 r_dihedral_angle_1_deg 7.617 r_angle_refined_deg 1.229 r_angle_other_deg 1.018 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.462 r_dihedral_angle_4_deg 22.151 r_dihedral_angle_3_deg 10.717 r_dihedral_angle_1_deg 7.617 r_angle_refined_deg 1.229 r_angle_other_deg 1.018 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1569 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data reduction PHASER phasing