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Crystal structure beta-glucanase SdGluc5_26A from Saccharophagus degradans in complex with tetrasaccharide A obtained by soaking
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A8O PDB ENTRY 5A8O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 0.2 M AMMONIUM SULPHATE, 0.1 M SODIUM CACODYLATE BUFFER PH 6.0, 25% (W/V) PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.11 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.702 α = 90 b = 143.702 β = 90 c = 143.702 γ = 90
Symmetry Space Group P 41 3 2
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 2013-05-31 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 1.9 47.9 100 0.1 19.5 9.6 40497 17.94
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 1.9 2 100 0.6 3.9 9.6
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 5A8O 1.9 47.95 38387 2051 99.97 0.13886 0.13766 0.1502 0.16098 0.1708 RANDOM 18.073
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.205 r_dihedral_angle_4_deg 15.727 r_dihedral_angle_3_deg 12.201 r_dihedral_angle_1_deg 6.094 r_angle_other_deg 1.427 r_angle_refined_deg 1.217 r_symmetry_vdw_refined 0.285 r_symmetry_hbond_refined 0.265 r_nbd_refined 0.248 r_nbtor_refined 0.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.205 r_dihedral_angle_4_deg 15.727 r_dihedral_angle_3_deg 12.201 r_dihedral_angle_1_deg 6.094 r_angle_other_deg 1.427 r_angle_refined_deg 1.217 r_symmetry_vdw_refined 0.285 r_symmetry_hbond_refined 0.265 r_nbd_refined 0.248 r_nbtor_refined 0.187 r_nbd_other 0.171 r_symmetry_vdw_other 0.134 r_xyhbond_nbd_refined 0.101 r_nbtor_other 0.082 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2775 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing