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The 1.7 A crystal structure of alpha-D-glucuronidase, a family-67 glycoside hydrolase from Bacillus stearothermophilus T-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other initial and partial model based on 2.4A resolution data (unpublished)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.1M Na-citrate pH 5.0, 14% PEG 4000, 12% Iso-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.84 56.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.57 α = 90 b = 73.57 β = 90 c = 329.96 γ = 90
Symmetry Space Group P 41 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 100 CCD ADSC QUANTUM 4 2000-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 1.00933 NSLS X8C
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 1.7 50 0.057 10.2 4 94808 17.8
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 1.7 1.73 60.7 0.382 3 3008
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT initial and partial model based on 2.4A resolution data (unpublished) 1.7 35.9 1 94808 91195 9105 93.5 0.176 0.176 0.203 RANDOM 20.7
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] 1.09 1.09 -2.18
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.49 c_scbond_it 1.69 c_mcangle_it 1.68 c_angle_deg 1.3 c_mcbond_it 1.13 c_improper_angle_d 0.77 c_bond_d 0.005 c_dihedral_angle_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5453 Nucleic Acid Atoms Solvent Atoms 650 Heterogen Atoms 78
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement