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Structure of the family GH92 alpha-mannosidase BT3130 from Bacteroides thetaiotaomicron
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 6.4 292 18% (w/v) PEG 3350, 0.1 M Bis-Tris propane, pH 6.4, 0.2 M NaBr
Crystal Properties Matthews coefficient Solvent content 4.08 69.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 272.301 α = 90 b = 272.301 β = 90 c = 190.047 γ = 120
Symmetry Space Group P 62 2 2
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 2014-08-14 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 2.5 49.67 99.8 0.21 0.218 0.06 0.998 18.6 25 142171 33.4
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 2.5 2.54 96.7 2 2.09 0.579 0.735 2.2 24.5
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 2.5 49.67 135113 7011 99.77 0.1826 0.18056 0.1852 0.22176 0.2253 RANDOM 50.745
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] 1.12 0.56 1.12 -3.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.164 r_dihedral_angle_4_deg 18.687 r_dihedral_angle_3_deg 14.634 r_dihedral_angle_1_deg 6.486 r_long_range_B_refined 6.107 r_long_range_B_other 6.107 r_mcangle_it 4.048 r_mcangle_other 4.048 r_scangle_other 3.725 r_mcbond_it 2.532
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.164 r_dihedral_angle_4_deg 18.687 r_dihedral_angle_3_deg 14.634 r_dihedral_angle_1_deg 6.486 r_long_range_B_refined 6.107 r_long_range_B_other 6.107 r_mcangle_it 4.048 r_mcangle_other 4.048 r_scangle_other 3.725 r_mcbond_it 2.532 r_mcbond_other 2.528 r_scbond_it 2.282 r_scbond_other 2.282 r_angle_refined_deg 1.318 r_angle_other_deg 0.961 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16609 Nucleic Acid Atoms Solvent Atoms 1293 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing