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Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482 in complex with Mannoimidazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other BT3990 APO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 25% PEG 1500 W/V, 0.1M MIBS (PH 6.0)
Crystal Properties Matthews coefficient Solvent content 2.66 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.19 α = 90 b = 152.39 β = 94.21 c = 221.45 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 2008-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 46.1 100 0.17 7.6 3.8 341632 2 35.1
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 2.37 100 0.47 2.01 3.8
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 BT3990 APO 2.25 218.22 324319 17260 99.98 0.20251 0.20038 0.2005 0.24227 0.241 RANDOM 23.718
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] -0.79 -0.19 -0.27 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.161 r_dihedral_angle_4_deg 16.275 r_dihedral_angle_3_deg 15.479 r_dihedral_angle_1_deg 6.132 r_scangle_it 1.746 r_angle_refined_deg 1.168 r_scbond_it 1.105 r_mcangle_it 0.673 r_mcbond_it 0.365 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.161 r_dihedral_angle_4_deg 16.275 r_dihedral_angle_3_deg 15.479 r_dihedral_angle_1_deg 6.132 r_scangle_it 1.746 r_angle_refined_deg 1.168 r_scbond_it 1.105 r_mcangle_it 0.673 r_mcbond_it 0.365 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 47675 Nucleic Acid Atoms Solvent Atoms 1868 Heterogen Atoms 234
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing