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Crystal structure of GH78 family rhamnosidase of Bacillus SP. GL1 AT 1.9 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SAD MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 13.5%(W/V) PEG 8000, 0.08M sodium cacodylate, 0.16M calcium acetate, 20%(V/V) glycerol, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.86 57.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.744 α = 90 b = 119.985 β = 90 c = 207.352 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU JUPITER 210 MIRRORS 2006-03-20 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD RIGAKU JUPITER 210 MIRRORS 2005-03-15 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.00 SPring-8 BL38B1 2 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.97916 SPring-8 BL38B1
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 1.9 49.4 98.8 0.066 11.2 5.3 188971 -3 17.4
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 1.9 1.97 91 0.407 2.1 4.6
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 SAD THROUGHOUT SAD MODEL 1.9 15 188458 18716 98.5 0.182 0.182 0.184 0.214 0.2147 RANDOM 30.1
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] 7.87 -3.69 -4.18
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 2.5 c_scbond_it 1.76 c_mcangle_it 1.71 c_angle_deg 1.3 c_mcbond_it 1.15 c_improper_angle_d 0.76 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 2.5 c_scbond_it 1.76 c_mcangle_it 1.71 c_angle_deg 1.3 c_mcbond_it 1.15 c_improper_angle_d 0.76 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14954 Nucleic Acid Atoms Solvent Atoms 1755 Heterogen Atoms 262
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELX phasing RESOLVE phasing CNS refinement PDB_EXTRACT data extraction HKL-2000 data scaling CNS phasing