5FQF

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 5FQE 

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.4549.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.03α = 90
b = 114.79β = 90
c = 134.7γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100MIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-1SSRLBL7-1

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
12.157099.80.14106.7722562
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)
12.152.2799.90.53.86.8

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 REPLACEMENTTHROUGHOUT5FQE2.1587.3768613357199.770.149620.147090.19818RANDOM21.851
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]
-0.81-0.481.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.537
r_dihedral_angle_4_deg14.474
r_dihedral_angle_3_deg12.982
r_dihedral_angle_1_deg6.819
r_mcangle_it2.442
r_scbond_it2.25
r_angle_refined_deg1.742
r_mcbond_it1.652
r_mcbond_other1.652
r_angle_other_deg1.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.537
r_dihedral_angle_4_deg14.474
r_dihedral_angle_3_deg12.982
r_dihedral_angle_1_deg6.819
r_mcangle_it2.442
r_scbond_it2.25
r_angle_refined_deg1.742
r_mcbond_it1.652
r_mcbond_other1.652
r_angle_other_deg1.012
r_chiral_restr0.102
r_bond_refined_d0.017
r_gen_planes_refined0.008
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 Atoms9428
Nucleic Acid Atoms
Solvent Atoms807
Heterogen Atoms105

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing