☰ Navigation Tabs
Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482 in complex with Thiomannobioside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WVX PDB ENTRY 2WVX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 20% 3350 PEG, 0.1 M (4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID) (PH 7.0), 0.15 M K2SO4
Crystal Properties Matthews coefficient Solvent content 2.75 55.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.24 α = 90 b = 153.11 β = 91.37 c = 185.21 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 CCD 2009-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.25 44.6 100 0.14 7.1 4.2 174544 2 25.3
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 2.25 2.37 99.9 0.47 3 3.9
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 PDB ENTRY 2WVX 2.25 185.16 165726 8730 99.95 0.18904 0.1875 0.1906 0.21817 0.2224 RANDOM 13.722
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] 0.07 0.02 -0.93 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.449 r_dihedral_angle_4_deg 18.188 r_dihedral_angle_3_deg 13.787 r_dihedral_angle_1_deg 5.896 r_scangle_it 2.589 r_scbond_it 1.583 r_angle_refined_deg 1.209 r_mcangle_it 0.885 r_mcbond_it 0.455 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.449 r_dihedral_angle_4_deg 18.188 r_dihedral_angle_3_deg 13.787 r_dihedral_angle_1_deg 5.896 r_scangle_it 2.589 r_scbond_it 1.583 r_angle_refined_deg 1.209 r_mcangle_it 0.885 r_mcbond_it 0.455 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other 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 23863 Nucleic Acid Atoms Solvent Atoms 1360 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing