5FR0

The details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from Clostridium perfringens


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5FQEPDB ENTRY 5FQE

Crystallization

Crystal Properties
Matthews coefficientSolvent content
1.9436.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.53α = 90
b = 99.53β = 90
c = 95.31γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-1CLSI08ID-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
11.7547.71000.1114.712.6553692
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)
11.751.781000.482.68.2

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 5FQE1.7595.3152619271399.960.182740.180740.22099RANDOM35.234
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]
1.030.511.03-3.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.94
r_dihedral_angle_4_deg14.898
r_dihedral_angle_3_deg13.882
r_dihedral_angle_1_deg6.779
r_mcangle_it3.692
r_scbond_it3.248
r_mcbond_it2.778
r_mcbond_other2.778
r_angle_refined_deg1.64
r_angle_other_deg0.869
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.94
r_dihedral_angle_4_deg14.898
r_dihedral_angle_3_deg13.882
r_dihedral_angle_1_deg6.779
r_mcangle_it3.692
r_scbond_it3.248
r_mcbond_it2.778
r_mcbond_other2.778
r_angle_refined_deg1.64
r_angle_other_deg0.869
r_chiral_restr0.1
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
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 Atoms4623
Nucleic Acid Atoms
Solvent Atoms415
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing