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Beta-glycosidase from Sulfolobus solfataricus in complex with glucoimidazole
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 SODIUM ACETATE, PH 4.6 0.2 AMMONIUM ACETATE, 10-13 MG/ML PROTEIN 25% ETHYLENE GLYCOL AS CRYO
Crystal Properties Matthews coefficient Solvent content 3.4 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.927 α = 90 b = 167.927 β = 90 c = 93.42 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 SAGITALLY FOCUSING GE(220) AND A MULTILAYER 2004-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 40 99.9 0.1 12.5 5.3 83599
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 0.4 3.94 5.1
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 2.14 145.86 79106 4163 99.4 0.178 0.176 0.1777 0.215 0.2163 RANDOM 35.88
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] -1.05 -0.52 -1.05 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.452 r_dihedral_angle_4_deg 18.378 r_dihedral_angle_3_deg 15.286 r_dihedral_angle_1_deg 6.439 r_scangle_it 2.58 r_scbond_it 1.783 r_angle_refined_deg 1.353 r_mcangle_it 1.206 r_mcbond_it 0.739 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.452 r_dihedral_angle_4_deg 18.378 r_dihedral_angle_3_deg 15.286 r_dihedral_angle_1_deg 6.439 r_scangle_it 2.58 r_scbond_it 1.783 r_angle_refined_deg 1.353 r_mcangle_it 1.206 r_mcbond_it 0.739 r_nbtor_refined 0.311 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.16 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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 7992 Nucleic Acid Atoms Solvent Atoms 876 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling