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Structure of beta-glycosidase from Sulfolobus solfataricus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GOW PDB ENTRY 1GOW
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 = 168.026 α = 90 b = 168.026 β = 90 c = 94.605 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 2003-04-15 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 2.02 40 99 0.069 17.3 4.89 99428
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 2.02 2.09 98.7 0.461 3.15 4.44
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 1GOW 2.02 141.42 93304 4900 97.8 0.196 0.194 0.1958 0.227 0.227 RANDOM 37.23
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] -1.73 -0.87 -1.73 2.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.988 r_scangle_it 3.037 r_scbond_it 1.981 r_angle_refined_deg 1.285 r_mcangle_it 1.24 r_mcbond_it 0.656 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.171 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.988 r_scangle_it 3.037 r_scbond_it 1.981 r_angle_refined_deg 1.285 r_mcangle_it 1.24 r_mcbond_it 0.656 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.171 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.096 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 7901 Nucleic Acid Atoms Solvent Atoms 866 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling