6TR3

Ruminococcus gnavus GH29 fucosidase E1_10125 in complex with fucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4OUE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M magnesium chloride, 25% PEG 3350, 0.1 M bis-tris pH 5.5 20mg/ml protein
Crystal Properties
Matthews coefficientSolvent content
2.0740.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.219α = 90
b = 48.643β = 115.02
c = 80.287γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97950DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim I (All)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
11.763.9499.10.0960.0546.93.15540719.629
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7397.50.7160.4091.12.9

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 REPLACEMENTTHROUGHOUT4OUE1.763.9452597280699.110.1840.18220.2187RANDOM25.309
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]
-0.11-0.49-0.110.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.989
r_dihedral_angle_4_deg17.634
r_dihedral_angle_3_deg12.239
r_dihedral_angle_1_deg5.449
r_angle_refined_deg1.215
r_angle_other_deg1.062
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.989
r_dihedral_angle_4_deg17.634
r_dihedral_angle_3_deg12.239
r_dihedral_angle_1_deg5.449
r_angle_refined_deg1.215
r_angle_other_deg1.062
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3978
Nucleic Acid Atoms
Solvent Atoms270
Heterogen Atoms17

Software

Software
Software NamePurpose
xia2data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
MOLREPphasing