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Crystal structure of human 5T4 (Wnt-activated inhibitory factor 1, Trophoblast glycoprotein)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZYJ PDB ENTRY 3ZYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 THE 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 coefficient Solvent content 1.9 34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.31 α = 90 b = 67.31 β = 90 c = 96.38 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING 2013-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.75 49.31 99.8 0.07 17.9 9.6 33062 3.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.8 99.2 0.81 3.1 9.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3ZYJ 1.75 43.94 31330 1674 99.76 0.18365 0.18172 0.1905 0.22153 0.2337 RANDOM 35.524
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] -1.32 3.22 -1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.2 r_dihedral_angle_4_deg 18.166 r_dihedral_angle_3_deg 12.762 r_dihedral_angle_1_deg 6.43 r_scbond_it 3.656 r_mcangle_it 2.814 r_mcbond_it 1.943 r_mcbond_other 1.942 r_angle_refined_deg 1.833 r_angle_other_deg 0.929
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.2 r_dihedral_angle_4_deg 18.166 r_dihedral_angle_3_deg 12.762 r_dihedral_angle_1_deg 6.43 r_scbond_it 3.656 r_mcangle_it 2.814 r_mcbond_it 1.943 r_mcbond_other 1.942 r_angle_refined_deg 1.833 r_angle_other_deg 0.929 r_chiral_restr 0.109 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 2201 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing