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Crystal structure of beta-glucanase SdGluc5_26A from Saccharophagus degradans in complex with tetrasaccharide A, form 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A8N PDB ENTRY 5A8N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 30% (W/V) PEG 4000, 0.1 M TRIS BUFFER PH 7.5, 0.2 M MGCL2
Crystal Properties Matthews coefficient Solvent content 2.29 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.048 α = 90 b = 60.384 β = 104.75 c = 130.326 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 PIXEL DECTRIS PILATUS 6M 2013-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.35 45.63 100 0.06 10.5 3.7 237302 11.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.42 99.9 0.44 2.6 3.7
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 PDB ENTRY 5A8N 1.35 45.44 225378 11901 99.98 0.13071 0.12938 0.1358 0.1561 0.1617 RANDOM 13.522
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] 0.2 0.14 -0.01 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.209 r_sphericity_free 31.427 r_dihedral_angle_4_deg 13.915 r_dihedral_angle_3_deg 10.999 r_rigid_bond_restr 8.621 r_sphericity_bonded 7.929 r_dihedral_angle_1_deg 6.297 r_angle_refined_deg 1.427 r_angle_other_deg 0.918 r_symmetry_vdw_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.209 r_sphericity_free 31.427 r_dihedral_angle_4_deg 13.915 r_dihedral_angle_3_deg 10.999 r_rigid_bond_restr 8.621 r_sphericity_bonded 7.929 r_dihedral_angle_1_deg 6.297 r_angle_refined_deg 1.427 r_angle_other_deg 0.918 r_symmetry_vdw_refined 0.316 r_nbd_refined 0.27 r_nbtor_refined 0.191 r_nbd_other 0.18 r_xyhbond_nbd_refined 0.158 r_symmetry_vdw_other 0.154 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.093 r_nbtor_other 0.082 r_xyhbond_nbd_other 0.054 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8326 Nucleic Acid Atoms Solvent Atoms 1740 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing