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Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 100MM MIBS BUFFER (PH 6.0), 10% V/V PEG 3.35K
Crystal Properties Matthews coefficient Solvent content 1.99 50.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.23 α = 90 b = 190.95 β = 96.97 c = 135.1 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 2008-07-25 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.9 49.3 97.6 0.08 18.3 7.3 248657 2 16.2
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 1.9 2 96.6 0.35 5 7
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 MAD THROUGHOUT NONE 1.9 133.63 234323 12380 97.53 0.1566 0.15502 0.1823 0.18647 0.2082 RANDOM 8.621
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] 0.45 -0.06 -0.34 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.714 r_dihedral_angle_4_deg 16.6 r_dihedral_angle_3_deg 14.276 r_dihedral_angle_1_deg 6.17 r_scangle_it 2.737 r_scbond_it 1.783 r_angle_refined_deg 1.333 r_mcangle_it 0.977 r_mcbond_it 0.572 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.714 r_dihedral_angle_4_deg 16.6 r_dihedral_angle_3_deg 14.276 r_dihedral_angle_1_deg 6.17 r_scangle_it 2.737 r_scbond_it 1.783 r_angle_refined_deg 1.333 r_mcangle_it 0.977 r_mcbond_it 0.572 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 23747 Nucleic Acid Atoms Solvent Atoms 2022 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling SHARP phasing