☰ Navigation Tabs
Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-D-glucal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UTF modified 4UTF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 292 3 M sodium acetate, pH 7.2
Crystal Properties Matthews coefficient Solvent content 2.27 45.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.684 α = 90 b = 108.684 β = 90 c = 67.641 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 2015-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.07 76.85 99.8 0.052 0.997 10.9 6.3 172107 13.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.07 1.09 96.5 1.748 0.33 0.6 4.9
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 modified 4UTF 1.07 76.85 163577 8530 99.79 0.12522 0.12438 0.1343 0.1412 0.1499 RANDOM 17.852
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] 0.04 0.04 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.047 r_sphericity_free 28.769 r_dihedral_angle_4_deg 19.581 r_dihedral_angle_3_deg 12.112 r_dihedral_angle_1_deg 9.036 r_sphericity_bonded 7.504 r_long_range_B_refined 2.929 r_long_range_B_other 2.445 r_scangle_other 1.822 r_rigid_bond_restr 1.617
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.047 r_sphericity_free 28.769 r_dihedral_angle_4_deg 19.581 r_dihedral_angle_3_deg 12.112 r_dihedral_angle_1_deg 9.036 r_sphericity_bonded 7.504 r_long_range_B_refined 2.929 r_long_range_B_other 2.445 r_scangle_other 1.822 r_rigid_bond_restr 1.617 r_scbond_it 1.579 r_scbond_other 1.579 r_angle_refined_deg 1.535 r_mcangle_other 1.503 r_mcangle_it 1.498 r_angle_other_deg 1.387 r_mcbond_it 1.134 r_mcbond_other 1.117 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2793 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing