3ZY5

Crystal structure of POFUT1 in complex with GDP-fucose (crystal-form-I)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZY2PDB ENTRY 3ZY2

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.9157

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.543α = 90
b = 42.53β = 107.63
c = 97.663γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKERESRFBM16

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
11.9656.01980.1112.197.06420272
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)
11.962.0694.70.4812.195.01

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 3ZY21.9693.083200576497.910.219150.2180.26752RANDOM23.265
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]
-0.81-0.091.39-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.22
r_dihedral_angle_3_deg17.067
r_dihedral_angle_4_deg16.84
r_dihedral_angle_1_deg6.397
r_scangle_it2.968
r_scbond_it1.938
r_angle_refined_deg1.432
r_mcangle_it1.327
r_mcbond_it0.742
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.22
r_dihedral_angle_3_deg17.067
r_dihedral_angle_4_deg16.84
r_dihedral_angle_1_deg6.397
r_scangle_it2.968
r_scbond_it1.938
r_angle_refined_deg1.432
r_mcangle_it1.327
r_mcbond_it0.742
r_chiral_restr0.101
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms2844
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing