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Structure of beta-glycosidase from Sulfolobus solfataricus in complex with 2-deoxy-2-fluoro-glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UWQ PDB ENTRY 1UWQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 11-14% PEG 4K 0.1 M NA ACETATE, 0.2 M AMMONIUM ACETATE, CRYO - 25% ETHYLENE GLYCOL, 10-13 MG/ML PROTEIN, pH 4.60
Crystal Properties Matthews coefficient Solvent content 3.4 63.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.605 α = 90 b = 167.605 β = 90 c = 95.448 γ = 120
Symmetry Space Group P 31 2 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 TOROIDAL MIRROR 2003-10-15 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 1.95 30 99.9 0.074 17.55 6.2 112688
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 1.95 2.02 100 0.339 6.03 6.2
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 PDB ENTRY 1UWQ 1.95 141.42 106013 5607 98.9 0.193 0.192 0.191 0.229 0.2281 RANDOM 32.68
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] -1.34 -0.67 -1.34 2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.917 r_scangle_it 3.281 r_scbond_it 2.107 r_mcangle_it 1.364 r_angle_refined_deg 1.342 r_mcbond_it 0.742 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.155 r_xyhbond_nbd_refined 0.121 r_symmetry_hbond_refined 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.917 r_scangle_it 3.281 r_scbond_it 2.107 r_mcangle_it 1.364 r_angle_refined_deg 1.342 r_mcbond_it 0.742 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.155 r_xyhbond_nbd_refined 0.121 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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 7873 Nucleic Acid Atoms Solvent Atoms 759 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing