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Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482
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% V/V 3350, 100MM MIBS BUFFER (PH 6.0)
Crystal Properties Matthews coefficient Solvent content 2.9 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.9 α = 90 b = 150.19 β = 90 c = 382.29 γ = 90
Symmetry Space Group P 21 21 21
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 2008-02-07 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 2.4 60 88.4 0.13 6.2 3.5 156201 2 39.1
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 2.4 2.53 89.3 0.49 2.1 3.5
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 PDB ENTRY 2WVX 2.4 191.14 130782 6859 88.12 0.20394 0.20112 0.2014 0.25718 0.2569 RANDOM 32.364
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] 2.26 1.04 -3.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.705 r_dihedral_angle_4_deg 18.027 r_dihedral_angle_3_deg 16.317 r_dihedral_angle_1_deg 6.367 r_scangle_it 2.376 r_scbond_it 1.496 r_angle_refined_deg 1.321 r_mcangle_it 0.945 r_mcbond_it 0.505 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.705 r_dihedral_angle_4_deg 18.027 r_dihedral_angle_3_deg 16.317 r_dihedral_angle_1_deg 6.367 r_scangle_it 2.376 r_scbond_it 1.496 r_angle_refined_deg 1.321 r_mcangle_it 0.945 r_mcbond_it 0.505 r_chiral_restr 0.085 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 23935 Nucleic Acid Atoms Solvent Atoms 792 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing