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Structure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.4 Angstrom resolution in the tetragonal form with NAD and glucose-6-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SE-MET STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 200 MM CALCIUM ACETATE, 100MM SODIUM ACETATE PH 4.6, 25% PEG500DME, 0.2MM NAD+, 1MM PNP-BETA-D-GLUCOSE-6-PHOSPHATE, 2MM MNS04. PROTEIN AT 5 MG/ML WITH THE COFACTORS IN THE SAME CONCENTRATION AS ABOVE.
Crystal Properties Matthews coefficient Solvent content 2.8 56.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.132 α = 90 b = 178.132 β = 90 c = 278.927 γ = 90
Symmetry Space Group P 43 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 120 CCD ADSC CCD 2003-06-15 M SINGLE WAVELENGTH
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 2.4 20 98.3 0.083 22.4 6.8 170857 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 2.4 2.49 98.3 0.461 3.5 5.5
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 SE-MET STRUCTURE 2.4 19.96 162307 8549 98.3 0.201 0.199 0.193 0.24 0.2298 RANDOM 21.05
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] -0.83 -0.83 1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.868 r_scangle_it 3.135 r_scbond_it 1.89 r_angle_refined_deg 1.425 r_mcangle_it 0.957 r_mcbond_it 0.439 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.868 r_scangle_it 3.135 r_scbond_it 1.89 r_angle_refined_deg 1.425 r_mcangle_it 0.957 r_mcbond_it 0.439 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 26560 Nucleic Acid Atoms Solvent Atoms 759 Heterogen Atoms 490
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling