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Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with sophorose, isofagomine, sulfate ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H3Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 PEG3350, calcium acetate, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.49 50.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.692 α = 90 b = 94.877 β = 100.81 c = 157.357 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 CCD ADSC QUANTUM 210r 2015-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00 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 2 50 96 0.127 3.7 3.7 168440
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 2.03 99 0.502 1.6 3.6 8322
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 5H3Z 2 48.27 160075 8340 99.73 0.16954 0.16774 0.1764 0.20406 0.2096 RANDOM 27.376
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 37.957 r_dihedral_angle_4_deg 15.874 r_dihedral_angle_3_deg 13.976 r_dihedral_angle_1_deg 6.723 r_long_range_B_other 5.746 r_long_range_B_refined 5.745 r_scangle_other 4.7 r_scbond_it 3.072 r_scbond_other 3.071 r_mcangle_it 3.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.957 r_dihedral_angle_4_deg 15.874 r_dihedral_angle_3_deg 13.976 r_dihedral_angle_1_deg 6.723 r_long_range_B_other 5.746 r_long_range_B_refined 5.745 r_scangle_other 4.7 r_scbond_it 3.072 r_scbond_other 3.071 r_mcangle_it 3.025 r_mcangle_other 3.025 r_mcbond_it 2.191 r_mcbond_other 2.191 r_angle_refined_deg 1.704 r_angle_other_deg 1.374 r_chiral_restr 0.107 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17836 Nucleic Acid Atoms Solvent Atoms 839 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing