6S22

Crystal structure of the TgGalNAc-T3 in complex with UDP, manganese and FGF23c


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NQA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291Morpheus precipitant mix 4, nitrate phosphate buffer and Morpheus buffer System 1
Crystal Properties
Matthews coefficientSolvent content
2.5752.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.957α = 90
b = 104.823β = 90
c = 143.466γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.97DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)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
11.9651.011000.0530.9968.9756142
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.962.071000.4140.6372.37.1

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 REPLACEMENTTHROUGHOUT5NQA1.9651.0153850221599.980.180460.179020.21589RANDOM35.312
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]
-0.76-0.531.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.533
r_dihedral_angle_4_deg20.267
r_dihedral_angle_3_deg15.782
r_long_range_B_refined9.304
r_long_range_B_other9.304
r_dihedral_angle_1_deg7.262
r_scangle_other6.898
r_mcangle_it4.883
r_mcangle_other4.883
r_scbond_it4.562
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.533
r_dihedral_angle_4_deg20.267
r_dihedral_angle_3_deg15.782
r_long_range_B_refined9.304
r_long_range_B_other9.304
r_dihedral_angle_1_deg7.262
r_scangle_other6.898
r_mcangle_it4.883
r_mcangle_other4.883
r_scbond_it4.562
r_scbond_other4.523
r_mcbond_it3.322
r_mcbond_other3.319
r_angle_refined_deg1.729
r_angle_other_deg1.37
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.01
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4367
Nucleic Acid Atoms46
Solvent Atoms303
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing