5A8O

Crystal structure of beta-glucanase SdGluc5_26A from Saccharophagus degradans in complex with cellotetraose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A8NPDB ENTRY 5A8N

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 = 143.773α = 90
b = 143.773β = 90
c = 143.773γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100DECTRIS P2013-05-31MSINGLE 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
12.347.921000.1117.59.52321223.16
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)
12.32.421000.5849.5

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 5A8N2.345.5121999117199.880.150670.149460.17282RANDOM26.595
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_deg37.268
r_dihedral_angle_4_deg14.347
r_dihedral_angle_3_deg12.52
r_dihedral_angle_1_deg5.814
r_angle_refined_deg1.191
r_angle_other_deg0.749
r_symmetry_vdw_refined0.269
r_nbd_refined0.238
r_symmetry_hbond_refined0.238
r_nbtor_refined0.188
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.268
r_dihedral_angle_4_deg14.347
r_dihedral_angle_3_deg12.52
r_dihedral_angle_1_deg5.814
r_angle_refined_deg1.191
r_angle_other_deg0.749
r_symmetry_vdw_refined0.269
r_nbd_refined0.238
r_symmetry_hbond_refined0.238
r_nbtor_refined0.188
r_xyhbond_nbd_other0.176
r_nbd_other0.17
r_symmetry_vdw_other0.15
r_xyhbond_nbd_refined0.128
r_nbtor_other0.081
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms291
Heterogen Atoms99

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing