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Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with cyclohexylmethyl-Glc-1,3-isofagomine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HMG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 3 M sodium acetate pH 6.6 - 7,4
Crystal Properties Matthews coefficient Solvent content 2.23 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.981 α = 90 b = 107.981 β = 90 c = 67.282 γ = 90
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-F 2011-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97630 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.09 76.35 95.9 0.059 0.065 0.027 0.997 12.5 5.1 153951 11.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.09 1.11 66.4 1.12 1.342 0.715 0.358 0.9 2.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6HMG 1.09 76.35 153946 7638 95.856 0.114 0.1133 0.1133 0.1355 0.1357 17.312
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] 0.098 0.098 -0.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.842 r_dihedral_angle_4_deg 16.775 r_dihedral_angle_3_deg 12.482 r_dihedral_angle_1_deg 6.652 r_rigid_bond_restr 4.737 r_lrange_it 4.268 r_scbond_it 4.24 r_scbond_other 4.24 r_scangle_it 4.118 r_scangle_other 4.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.842 r_dihedral_angle_4_deg 16.775 r_dihedral_angle_3_deg 12.482 r_dihedral_angle_1_deg 6.652 r_rigid_bond_restr 4.737 r_lrange_it 4.268 r_scbond_it 4.24 r_scbond_other 4.24 r_scangle_it 4.118 r_scangle_other 4.118 r_lrange_other 3.929 r_mcangle_other 2.864 r_mcangle_it 2.855 r_mcbond_it 2.352 r_mcbond_other 2.351 r_angle_refined_deg 1.93 r_angle_other_deg 1.566 r_nbd_refined 0.227 r_symmetry_nbd_refined 0.227 r_symmetry_nbd_other 0.195 r_nbd_other 0.194 r_nbtor_refined 0.191 r_symmetry_xyhbond_nbd_refined 0.165 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.12 r_symmetry_nbtor_other 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2906 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing