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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 PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.1 α = 90 b = 115.1 β = 113.4 c = 99.5 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 2007-09-20 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 1.9 49.09 99.9 0.11 12 3.6 150972 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 2 100 0.43 2.5 3.8
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 1.9 91.29 140442 7418 99.9 0.179 0.177 0.1765 0.231 0.2309 RANDOM 22.8
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] -1.2 -1.61 0.62 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.261 r_dihedral_angle_4_deg 19.181 r_dihedral_angle_3_deg 14.466 r_dihedral_angle_1_deg 6.888 r_scangle_it 3.276 r_scbond_it 2.238 r_angle_refined_deg 1.575 r_mcangle_it 1.312 r_mcbond_it 0.786 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.261 r_dihedral_angle_4_deg 19.181 r_dihedral_angle_3_deg 14.466 r_dihedral_angle_1_deg 6.888 r_scangle_it 3.276 r_scbond_it 2.238 r_angle_refined_deg 1.575 r_mcangle_it 1.312 r_mcbond_it 0.786 r_chiral_restr 0.11 r_bond_refined_d 0.016 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 13500 Nucleic Acid Atoms Solvent Atoms 1230 Heterogen Atoms 262
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling