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Structure of E70A mutant of Rex8A from Paenibacillus barcinonensis complexed with 3(3)-alpha-L-arabinofuranosyl-xylotetraose.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SRD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 20% PEG 3350, 0.2M Potassium thiocyanate, 0.1M Bis Tris propane pH 7.5. Microseeding. Co-crystallization: 5 mM 3(3)-alpha-L-arabinofuranosyl-xylotetraose.
Cryoprotectant: 25% Glycerol.
Crystal Properties Matthews coefficient Solvent content 2.29 46.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.295 α = 90 b = 82.72 β = 90 c = 465.317 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 6M KB Mirrors 2019-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979260 ALBA XALOC
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 1.85 46.62 97.2 0.153 0.162 0.052 0.992 8 7.4 129847
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 1.86 1.89 80.7 0.658 0.768 0.377 0.568 1 3.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6SRD 1.86 46.62 123280 6472 95.69 0.2398 0.2385 0.2633 0.2913 RANDOM 33.218
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] -8.51 -6.95 15.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.423 r_dihedral_angle_3_deg 14.792 r_dihedral_angle_4_deg 13.273 r_dihedral_angle_1_deg 6.66 r_angle_refined_deg 1.417 r_angle_other_deg 1.24 r_chiral_restr 0.081 r_bond_refined_d 0.006 r_bond_other_d 0.004 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.423 r_dihedral_angle_3_deg 14.792 r_dihedral_angle_4_deg 13.273 r_dihedral_angle_1_deg 6.66 r_angle_refined_deg 1.417 r_angle_other_deg 1.24 r_chiral_restr 0.081 r_bond_refined_d 0.006 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12535 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing