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Structure of wild type Bt4394, a GH20 family sulfoglycosidase, in complex with 6S-GlcNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RCN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 282 10 mM of 4MU-6S-GlcNAc with 10 mg/mL protein in the buffer of 25 mM PH 8.0, =300 mM NaCl was mixed with 0.1 M BICINE, pH 8.5, 20 % (w/v) PEG 10000 at 1:1 to carry on co-crystallization.
Crystal Properties Matthews coefficient Solvent content 2.13 42.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.5 α = 90 b = 125.596 β = 90.631 c = 84.64 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2019-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979191 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 70.19 97.4 0.097 0.996 11.5 6.8 145268
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 1.005 0.584 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3rcn 1.55 50.483 145227 7467 97.224 0.144 0.1417 0.1401 0.1844 0.1831 22.979
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] -0.449 0.328 1.723 -1.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.207 r_dihedral_angle_4_deg 18.414 r_dihedral_angle_3_deg 12.863 r_dihedral_angle_1_deg 6.466 r_lrange_it 3.44 r_scangle_it 3.069 r_scbond_it 2.625 r_mcangle_it 2.284 r_mcbond_it 1.762 r_rigid_bond_restr 1.467
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.207 r_dihedral_angle_4_deg 18.414 r_dihedral_angle_3_deg 12.863 r_dihedral_angle_1_deg 6.466 r_lrange_it 3.44 r_scangle_it 3.069 r_scbond_it 2.625 r_mcangle_it 2.284 r_mcbond_it 1.762 r_rigid_bond_restr 1.467 r_angle_refined_deg 1.217 r_nbtor_refined 0.315 r_symmetry_nbd_refined 0.24 r_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.131 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.092 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8495 Nucleic Acid Atoms Solvent Atoms 566 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction