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Structural and biochemical evidence for a boat-like transition state in beta-mannosidases
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JE8 PDB ENTRY 2JE8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 14% PEG 3350, 0.2M NABR, 0.1M MES BUFFER PH 6.4
Crystal Properties Matthews coefficient Solvent content 2.5 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.118 α = 90 b = 115.692 β = 113.17 c = 99.643 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 120 CCD ADSC CCD 2007-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.3 57.83 100 0.25 8 4.9 84327 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 2.3 2.4 100 0.47 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 2JE8 2.3 52.49 80084 4219 100 0.173 0.169 0.1689 0.247 0.2457 RANDOM 19.64
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] -1.44 -0.94 0.15 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.573 r_dihedral_angle_4_deg 19.854 r_dihedral_angle_3_deg 15.9 r_dihedral_angle_1_deg 7.184 r_scangle_it 3.525 r_scbond_it 2.299 r_angle_refined_deg 1.69 r_mcangle_it 1.357 r_mcbond_it 0.748 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.573 r_dihedral_angle_4_deg 19.854 r_dihedral_angle_3_deg 15.9 r_dihedral_angle_1_deg 7.184 r_scangle_it 3.525 r_scbond_it 2.299 r_angle_refined_deg 1.69 r_mcangle_it 1.357 r_mcbond_it 0.748 r_chiral_restr 0.115 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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 13571 Nucleic Acid Atoms Solvent Atoms 949 Heterogen Atoms 187
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling