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Crystal structure of the native form of beta-glucanase SdGluc5_26A from Saccharophagus degradans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A8M WWPDB ENTRY 5A8M
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 3.13 60.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.341 α = 90 b = 143.341 β = 90 c = 143.341 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 2012-02-03 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 2.05 32.8 100 0.09 19.4 13 32184 29.48
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 2.05 2.16 100 0.78 3.2 13.1
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 WWPDB ENTRY 5A8M 2.05 32.91 30488 1628 99.94 0.15259 0.15113 0.17997 0.1753 RANDOM 31.695
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 36.909 r_dihedral_angle_4_deg 14.849 r_dihedral_angle_3_deg 11.941 r_dihedral_angle_1_deg 6.014 r_angle_refined_deg 1.282 r_angle_other_deg 0.755 r_symmetry_vdw_refined 0.285 r_symmetry_hbond_refined 0.252 r_nbd_refined 0.248 r_nbtor_refined 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.909 r_dihedral_angle_4_deg 14.849 r_dihedral_angle_3_deg 11.941 r_dihedral_angle_1_deg 6.014 r_angle_refined_deg 1.282 r_angle_other_deg 0.755 r_symmetry_vdw_refined 0.285 r_symmetry_hbond_refined 0.252 r_nbd_refined 0.248 r_nbtor_refined 0.19 r_nbd_other 0.173 r_symmetry_vdw_other 0.146 r_xyhbond_nbd_refined 0.106 r_nbtor_other 0.084 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.003 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 305 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing