5A8M

Crystal structure of the selenomethionine derivative of beta-glucanase SdGluc5_26A from Saccharophagus degradans


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.525% (W/V) PEG3350, 0.2 M MGCL2, 0.1 M BIS-TRIS BUFFER PH 6.5.
Crystal Properties
Matthews coefficientSolvent content
2.9458.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.605α = 90
b = 142.605β = 90
c = 136.277γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 1

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
11.8647.5399.40.19.56116426
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)
11.861.9699.20.383.55.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUTNONE1.8647.33110515584199.170.144450.143360.16513RANDOM18.061
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]
0.130.13-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.956
r_dihedral_angle_4_deg16.236
r_dihedral_angle_3_deg11.397
r_dihedral_angle_1_deg6.057
r_angle_refined_deg1.388
r_angle_other_deg1.043
r_symmetry_vdw_refined0.319
r_symmetry_hbond_refined0.299
r_nbd_refined0.264
r_nbtor_refined0.187
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.956
r_dihedral_angle_4_deg16.236
r_dihedral_angle_3_deg11.397
r_dihedral_angle_1_deg6.057
r_angle_refined_deg1.388
r_angle_other_deg1.043
r_symmetry_vdw_refined0.319
r_symmetry_hbond_refined0.299
r_nbd_refined0.264
r_nbtor_refined0.187
r_symmetry_vdw_other0.18
r_nbd_other0.176
r_xyhbond_nbd_refined0.117
r_chiral_restr0.089
r_nbtor_other0.085
r_xyhbond_nbd_other0.06
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.005
r_gen_planes_other0.004
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 AtomsNumber
Protein Atoms8348
Nucleic Acid Atoms
Solvent Atoms1223
Heterogen Atoms157

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
SHELXphasing