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Crystal structure of GH30 Streptomyces avermitilis endo-beta-1,6-galactanase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
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 39.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.128 α = 90 b = 50.128 β = 90 c = 331.431 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 315 2013-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.9 100 100 0.144 17 13.8 35216
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 1.97 0.728 4.4
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 1.9 49.564 34947 1752 99.971 0.154 0.1524 0.166 0.1837 0.1919 RANDOM 21.973
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] 0.005 0.005 -0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.568 r_dihedral_angle_3_deg 10.707 r_dihedral_angle_1_deg 7.008 r_dihedral_angle_2_deg 5.664 r_lrange_it 4.534 r_lrange_other 4.408 r_scangle_it 2.905 r_scangle_other 2.905 r_scbond_it 2.043 r_scbond_other 2.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.568 r_dihedral_angle_3_deg 10.707 r_dihedral_angle_1_deg 7.008 r_dihedral_angle_2_deg 5.664 r_lrange_it 4.534 r_lrange_other 4.408 r_scangle_it 2.905 r_scangle_other 2.905 r_scbond_it 2.043 r_scbond_other 2.043 r_mcangle_other 1.876 r_mcangle_it 1.875 r_mcbond_it 1.24 r_angle_refined_deg 1.236 r_mcbond_other 1.234 r_angle_other_deg 0.475 r_nbd_other 0.224 r_symmetry_nbd_refined 0.201 r_nbd_refined 0.199 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.168 r_xyhbond_nbd_refined 0.134 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.064 r_gen_planes_refined 0.006 r_bond_refined_d 0.004 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 257 Heterogen Atoms 133
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing