4CNM

Crystal structure of human 5T4 (Wnt-activated inhibitory factor 1, Trophoblast glycoprotein)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1THE CRYSTALLIZATION DROP CONTAINED 100 NL OF CONCENTRATED 5T4 (5.5 MG/ML), 100 NL OF 25% W/V POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M CITRATE PH 3.5, AND 0.5 NL OF 0.1 M NAOH
Crystal Properties
Matthews coefficientSolvent content
1.934

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.31α = 90
b = 67.31β = 90
c = 96.38γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING2013-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.7549.3199.80.0717.99.6330623.1
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)
11.751.899.20.813.19.3

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 3ZYJ1.7543.9431330167499.760.183650.181720.22153RANDOM35.524
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]
-1.323.22-1.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.2
r_dihedral_angle_4_deg18.166
r_dihedral_angle_3_deg12.762
r_dihedral_angle_1_deg6.43
r_scbond_it3.656
r_mcangle_it2.814
r_mcbond_it1.943
r_mcbond_other1.942
r_angle_refined_deg1.833
r_angle_other_deg0.929
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.2
r_dihedral_angle_4_deg18.166
r_dihedral_angle_3_deg12.762
r_dihedral_angle_1_deg6.43
r_scbond_it3.656
r_mcangle_it2.814
r_mcbond_it1.943
r_mcbond_other1.942
r_angle_refined_deg1.833
r_angle_other_deg0.929
r_chiral_restr0.109
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 Atoms2201
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing