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Metagenomic glucose-tolerant glycosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1 M Tris-HCl buffer, 1.3 M lithium sulfate, 0.01 M nickel chloride
Crystal Properties Matthews coefficient Solvent content 3.31 62.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.427 α = 90 b = 202.427 β = 90 c = 202.427 γ = 90
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 RAYONIX MX300HE 2015-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.75 50 98 0.091 0.095 0.027 9.5 8.5 134784
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 93.3 0.401 0.473 0.243 3.2
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 2JIE 1.75 30 128017 6676 97.94 0.20875 0.20633 0.2134 0.25477 0.2578 RANDOM 20.865
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.815 r_sphericity_free 26.931 r_dihedral_angle_4_deg 14.987 r_dihedral_angle_3_deg 14.544 r_sphericity_bonded 10.097 r_scangle_other 5.113 r_dihedral_angle_1_deg 4.84 r_long_range_B_refined 4.658 r_long_range_B_other 4.599 r_scbond_it 4.469
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.815 r_sphericity_free 26.931 r_dihedral_angle_4_deg 14.987 r_dihedral_angle_3_deg 14.544 r_sphericity_bonded 10.097 r_scangle_other 5.113 r_dihedral_angle_1_deg 4.84 r_long_range_B_refined 4.658 r_long_range_B_other 4.599 r_scbond_it 4.469 r_scbond_other 4.436 r_rigid_bond_restr 4.285 r_mcangle_other 3.459 r_mcangle_it 3.455 r_mcbond_it 2.909 r_mcbond_other 2.892 r_angle_refined_deg 1.84 r_angle_other_deg 1.128 r_chiral_restr 0.129 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7206 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing