5A94

Crystal structure of beta-Glucanase SdGluc5_26A from Saccharophagus degradans in complex with tetrasaccharide A, form 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.530% (W/V) PEG 4000, 0.1 M TRIS BUFFER PH 7.5, 0.2 M MGCL2
Crystal Properties
Matthews coefficientSolvent content
2.4850.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 188.643α = 90
b = 132.753β = 133.78
c = 131.352γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-09-11MSINGLE 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
1247.531000.16.63.515711419.67
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)
122.1199.90.372.63.6

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTWWPDB ENTRY 5A8N1.9947.42149108800198.220.17950.178910.19038RANDOM23.785
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]
-0.9314.92-5.416.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.022
r_dihedral_angle_4_deg15.511
r_dihedral_angle_3_deg12.529
r_dihedral_angle_1_deg5.655
r_angle_refined_deg1.282
r_angle_other_deg1.15
r_symmetry_vdw_refined0.31
r_symmetry_vdw_other0.257
r_nbd_refined0.241
r_symmetry_hbond_refined0.235
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.022
r_dihedral_angle_4_deg15.511
r_dihedral_angle_3_deg12.529
r_dihedral_angle_1_deg5.655
r_angle_refined_deg1.282
r_angle_other_deg1.15
r_symmetry_vdw_refined0.31
r_symmetry_vdw_other0.257
r_nbd_refined0.241
r_symmetry_hbond_refined0.235
r_nbtor_refined0.189
r_nbd_other0.183
r_symmetry_hbond_other0.156
r_xyhbond_nbd_other0.132
r_xyhbond_nbd_refined0.129
r_nbtor_other0.085
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.006
r_gen_planes_other0.005
r_metal_ion_refined
r_metal_ion_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 Atoms16604
Nucleic Acid Atoms
Solvent Atoms1541
Heterogen Atoms216

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing