☰ Navigation Tabs
Structure of the family GH92 alpha-mannosidase BT3965 from Bacteroides thetaiotaomicron in complex with Mannoimidazole (ManI)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 20% w/v PEG 3350, 0.2 M NaNO3
Crystal Properties Matthews coefficient Solvent content 2.13 42.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.507 α = 90 b = 186.904 β = 91.74 c = 95.05 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 PIXEL DECTRIS PILATUS 2M 2014-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
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 1.9 46.73 96.1 0.155 0.203 0.129 0.989 7.1 4.4 216402 14.7
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 1.9 1.93 96.4 0.941 1.229 0.785 0.506 1.4 4.3
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 2WVY 1.9 46.73 205642 10713 96 0.17829 0.17674 0.1855 0.20766 0.2142 RANDOM 23.019
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] 2.02 -0.37 -1.35 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.181 r_dihedral_angle_4_deg 14.772 r_dihedral_angle_3_deg 13.321 r_dihedral_angle_1_deg 6.826 r_long_range_B_refined 4.344 r_long_range_B_other 4.344 r_scangle_other 2.537 r_mcangle_it 2.171 r_mcangle_other 2.171 r_scbond_it 1.619
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.181 r_dihedral_angle_4_deg 14.772 r_dihedral_angle_3_deg 13.321 r_dihedral_angle_1_deg 6.826 r_long_range_B_refined 4.344 r_long_range_B_other 4.344 r_scangle_other 2.537 r_mcangle_it 2.171 r_mcangle_other 2.171 r_scbond_it 1.619 r_scbond_other 1.619 r_angle_refined_deg 1.42 r_mcbond_it 1.412 r_mcbond_other 1.412 r_angle_other_deg 0.98 r_chiral_restr 0.094 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 24089 Nucleic Acid Atoms Solvent Atoms 2305 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing