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X-ray crystal structure of LsAA9B (xylotetraose soak)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EJA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 0.1M HEPES/MOPS pH 7.5
24 %(w/v) PEGMME 500
12 %(w/v) PEG 20000
0.03 M CaCl2
0.03 M MgCl2
Crystal soaked with a 0.8 M Xylotetraose solution for 1 hour and 20 min.
Crystal Properties Matthews coefficient Solvent content 2.18 43.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.41 α = 90 b = 72.79 β = 90 c = 78.59 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 PIXEL DECTRIS PILATUS 6M 2015-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9760 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.4 40 100 0.1 0.999 13.57 7.17 40817
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.44 100 1.56 0.454 1.36 7.27
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3EJA 1.4 39.33 38750 2067 99.93 0.13519 0.13306 0.1328 0.17513 0.1743 RANDOM 19.084
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] -0.56 2.8 -2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.819 r_dihedral_angle_4_deg 23.198 r_sphericity_bonded 22.841 r_sphericity_free 20.121 r_dihedral_angle_3_deg 11.218 r_rigid_bond_restr 10.793 r_dihedral_angle_1_deg 6.521 r_long_range_B_refined 5.828 r_long_range_B_other 5.734 r_scangle_other 5.532
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.819 r_dihedral_angle_4_deg 23.198 r_sphericity_bonded 22.841 r_sphericity_free 20.121 r_dihedral_angle_3_deg 11.218 r_rigid_bond_restr 10.793 r_dihedral_angle_1_deg 6.521 r_long_range_B_refined 5.828 r_long_range_B_other 5.734 r_scangle_other 5.532 r_scbond_it 4.617 r_scbond_other 4.617 r_mcangle_other 3.079 r_mcangle_it 3.078 r_mcbond_other 2.388 r_mcbond_it 2.379 r_angle_refined_deg 1.811 r_angle_other_deg 1.091 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1641 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction XSCALE data scaling MOLREP phasing Coot model building