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A X-ray Crystallographic Structure Model of a Glycoside Hydrolase (GH) Family 39 (GH39)-like Enzyme Encoded within a Xylan Utilization Locus of the pSOL1 Megaplasmid of Clostridium acetobutylicum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U22
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Hampton Research PEGRx HT: Condition 80 (G8): 0.2 M Sodium Formate, 0.1 M BICINE pH 8.5, 20% PEG5000 MME. This condition was extensively refined and the crystal which generated the data for this deposit consisted of the same, but had pH adjusted to 8.3.
Crystal Properties Matthews coefficient Solvent content 1.95 36.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.407 α = 90 b = 88.245 β = 90 c = 106.593 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 105 PIXEL DECTRIS PILATUS3 2M Rhodium coated silicon single crystal 2018-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
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 1.55 100 94.3 0.155 0.162 0.047 0.995 4.7 11 96886
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 1.55 1.61 60.6 1.53 1.72 0.751 0.277 3.8
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 1.55 35.89 78644 4294 80.48 0.14429 0.14238 0.1562 0.17987 0.1896 RANDOM 17.324
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] -0.31 -0.25 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.596 r_dihedral_angle_4_deg 19.689 r_dihedral_angle_3_deg 12.399 r_dihedral_angle_1_deg 6.997 r_long_range_B_refined 5.726 r_long_range_B_other 5.576 r_scangle_other 3.193 r_scbond_it 2.196 r_scbond_other 2.058 r_mcangle_other 1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.596 r_dihedral_angle_4_deg 19.689 r_dihedral_angle_3_deg 12.399 r_dihedral_angle_1_deg 6.997 r_long_range_B_refined 5.726 r_long_range_B_other 5.576 r_scangle_other 3.193 r_scbond_it 2.196 r_scbond_other 2.058 r_mcangle_other 1.92 r_mcangle_it 1.919 r_angle_refined_deg 1.539 r_angle_other_deg 1.458 r_mcbond_it 1.304 r_mcbond_other 1.304 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6250 Nucleic Acid Atoms Solvent Atoms 872 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling HKL-3000 data reduction PHASER phasing