5A8Q

Crystal structure beta-glucanase SdGluc5_26A from Saccharophagus degradans in complex with tetrasaccharide A obtained by soaking


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
160.2 M AMMONIUM SULPHATE, 0.1 M SODIUM CACODYLATE BUFFER PH 6.0, 25% (W/V) PEG 8000
Crystal Properties
Matthews coefficientSolvent content
3.1160.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.702α = 90
b = 143.702β = 90
c = 143.702γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-05-31MSINGLE 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
11.947.91000.119.59.64049717.94
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)
11.921000.63.99.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 5A8O1.947.9538387205199.970.138860.137660.16098RANDOM18.073
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.205
r_dihedral_angle_4_deg15.727
r_dihedral_angle_3_deg12.201
r_dihedral_angle_1_deg6.094
r_angle_other_deg1.427
r_angle_refined_deg1.217
r_symmetry_vdw_refined0.285
r_symmetry_hbond_refined0.265
r_nbd_refined0.248
r_nbtor_refined0.187
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.205
r_dihedral_angle_4_deg15.727
r_dihedral_angle_3_deg12.201
r_dihedral_angle_1_deg6.094
r_angle_other_deg1.427
r_angle_refined_deg1.217
r_symmetry_vdw_refined0.285
r_symmetry_hbond_refined0.265
r_nbd_refined0.248
r_nbtor_refined0.187
r_nbd_other0.171
r_symmetry_vdw_other0.134
r_xyhbond_nbd_refined0.101
r_nbtor_other0.082
r_chiral_restr0.074
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
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 Atoms2775
Nucleic Acid Atoms
Solvent Atoms421
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing