Crystal structure of selenomethionine labelled Streptomyces avermitilis endo-beta-1,6-galactanase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.629317% PEG4000, 20% isopropanol, 0.1 M Sodium citrate pH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.1141.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.173α = 90
b = 233.013β = 94.855
c = 87.885γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2102009-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A0.97920Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1210098.40.14914.48.2114201
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.070.3924.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.00143.769113931570198.2690.1720.16930.17640.21480.221RANDOM14.035
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]
-0.0340.0110.0180.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.218
r_dihedral_angle_3_deg11.104
r_dihedral_angle_1_deg7.035
r_dihedral_angle_2_deg5.735
r_lrange_it3.567
r_scangle_it1.619
r_mcangle_it1.37
r_angle_refined_deg1.291
r_scbond_it1.019
r_mcbond_it0.813
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.218
r_dihedral_angle_3_deg11.104
r_dihedral_angle_1_deg7.035
r_dihedral_angle_2_deg5.735
r_lrange_it3.567
r_scangle_it1.619
r_mcangle_it1.37
r_angle_refined_deg1.291
r_scbond_it1.019
r_mcbond_it0.813
r_nbtor_refined0.304
r_symmetry_nbd_refined0.231
r_nbd_refined0.192
r_symmetry_xyhbond_nbd_refined0.166
r_xyhbond_nbd_refined0.141
r_chiral_restr0.093
r_gen_planes_refined0.006
r_bond_refined_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14356
Nucleic Acid Atoms
Solvent Atoms1487
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing