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Crystal structure of GH30 endo-beta-1,6-galactanase from Streptomyces avermitilis soaked with Gal-beta1,6-Gal-beta1,6-Gal.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 24TD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.6 M ammonium sulfate, 0.1 M MES pH 6.5, 10% dioxane
Crystal Properties Matthews coefficient Solvent content 2.03 39.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.636 α = 90 b = 50.636 β = 90 c = 330.766 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2013-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
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 1.7 100 97.7 0.193 16.1 13.6 48189
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 1.7 1.74 0.754 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.7 48.464 48045 2416 97.714 0.15 0.1486 0.1631 0.1808 0.1897 RANDOM 9.731
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] -0.048 -0.048 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.024 r_dihedral_angle_3_deg 10.323 r_dihedral_angle_1_deg 7.229 r_dihedral_angle_2_deg 6.208 r_lrange_it 3.387 r_lrange_other 2.888 r_angle_refined_deg 1.169 r_scangle_it 1.153 r_scangle_other 1.153 r_mcangle_it 0.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.024 r_dihedral_angle_3_deg 10.323 r_dihedral_angle_1_deg 7.229 r_dihedral_angle_2_deg 6.208 r_lrange_it 3.387 r_lrange_other 2.888 r_angle_refined_deg 1.169 r_scangle_it 1.153 r_scangle_other 1.153 r_mcangle_it 0.814 r_mcangle_other 0.814 r_scbond_it 0.712 r_scbond_other 0.712 r_mcbond_it 0.481 r_mcbond_other 0.477 r_angle_other_deg 0.473 r_nbd_refined 0.2 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.178 r_nbd_other 0.162 r_symmetry_xyhbond_nbd_refined 0.134 r_xyhbond_nbd_refined 0.129 r_symmetry_nbd_refined 0.089 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.062 r_gen_planes_refined 0.005 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3547 Nucleic Acid Atoms Solvent Atoms 574 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing