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Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with Glucose-1,3-deoxymannojirimycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other PREVIOUSLY SOLVED STRUCTURE OF CLOSELY RELATED HOMOLOG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.1 M SODIUM ACETATE PH 4.9, 20% W/V PEG 2000 MME, 1.6% PGA-LM (POLY-GAMMA-GLUTAMIC ACID LOW MOLECULAR WEIGHT)
Crystal Properties Matthews coefficient Solvent content 3.52 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 222.478 α = 90 b = 222.478 β = 90 c = 84.715 γ = 120
Symmetry Space Group P 31 2 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 PIXEL DECTRIS PILATUS 6M MIRRORS 2011-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 99.8 0.15 11.4 10.1 161771 2 26.2
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 2.11 98.5 0.98 2.4 9.8
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 PREVIOUSLY SOLVED STRUCTURE OF CLOSELY RELATED HOMOLOG 2 46.49 153609 8060 99.73 0.176 0.17464 0.1746 0.20153 0.201 RANDOM 30.933
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] 0.12 0.06 0.12 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.237 r_dihedral_angle_4_deg 15.441 r_dihedral_angle_3_deg 14.586 r_dihedral_angle_1_deg 5.938 r_angle_refined_deg 1.242 r_mcangle_it 1.242 r_nbtor_refined 0.313 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.196 r_symmetry_hbond_refined 0.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.237 r_dihedral_angle_4_deg 15.441 r_dihedral_angle_3_deg 14.586 r_dihedral_angle_1_deg 5.938 r_angle_refined_deg 1.242 r_mcangle_it 1.242 r_nbtor_refined 0.313 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.196 r_symmetry_hbond_refined 0.182 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_mcbond_it 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other 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 10965 Nucleic Acid Atoms Solvent Atoms 1374 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing