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STRUCTURE OF THE FAMILY GH92 INVERTING MANNOSIDASE BT2199 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 10% V/V 2-METHYL-2, 4-PENTANEDIOL, 1.2 M C3H2O4NA2 AND 0.1M 1, 3-BIS(TRIS(HYDROXYMETHYL)METHYLAMINO)PROPANETE (PH 7.5)
Crystal Properties Matthews coefficient Solvent content 2.84 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.934 α = 90 b = 163.765 β = 90 c = 115.533 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC CCD 2008-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 60 100 0.13 14 8.2 139549 2 28.9
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 0.5 4 8.3
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 PDB ENTRY 2WVX 2.26 115.47 129149 6823 98.35 0.17064 0.16876 0.1773 0.20656 0.2144 RANDOM 16.105
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] 1.28 -0.88 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.582 r_dihedral_angle_4_deg 14.595 r_dihedral_angle_3_deg 14.285 r_dihedral_angle_1_deg 9.402 r_scangle_it 2.552 r_scbond_it 1.546 r_angle_refined_deg 1.207 r_mcangle_it 0.911 r_mcbond_it 0.463 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.582 r_dihedral_angle_4_deg 14.595 r_dihedral_angle_3_deg 14.285 r_dihedral_angle_1_deg 9.402 r_scangle_it 2.552 r_scbond_it 1.546 r_angle_refined_deg 1.207 r_mcangle_it 0.911 r_mcbond_it 0.463 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 17346 Nucleic Acid Atoms Solvent Atoms 1080 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing