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Structure of beta-glycosidase from Sulfolobus solfataricus in complex with 2-deoxy-2-fluoro-galactose
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 4.6
Crystal Properties Matthews coefficient Solvent content 3.4 63.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.059 α = 90 b = 168.059 β = 90 c = 95.773 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 QUANTUM 210 TOROIDAL MIRROR 2003-05-15 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 2.15 30 99.9 0.117 10.1 5.89 85809
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 2.15 2.23 100 0.455 2.82 5.86
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 2.14 141.42 81104 4268 98.9 0.192 0.19 0.1893 0.231 0.2259 RANDOM 41.05
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] -1.53 -0.77 -1.53 2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.094 r_scangle_it 3.303 r_scbond_it 2.126 r_mcangle_it 1.379 r_angle_refined_deg 1.357 r_mcbond_it 0.718 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.171 r_symmetry_hbond_refined 0.148 r_xyhbond_nbd_refined 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.094 r_scangle_it 3.303 r_scbond_it 2.126 r_mcangle_it 1.379 r_angle_refined_deg 1.357 r_mcbond_it 0.718 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.171 r_symmetry_hbond_refined 0.148 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.098 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 7881 Nucleic Acid Atoms Solvent Atoms 626 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing