1V7N

Human Thrombopoietin Functional Domain Complexed To Neutralizing Antibody TN1 Fab


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629320% PEG 4000, 0.1M potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4248.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.038α = 90
b = 46.582β = 90.28
c = 191.359γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100DIFFRACTOMETERWEISSENBERG1998-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6B1.0Photon FactoryBL-6B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
13.360980.09831.635598-0.536.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.33.42970.2141.11.63468

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 1IAI3.357.6334015180198.450.174050.167080.30477RANDOM29.767
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]
-1.72-0.332.25-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg11.133
r_scangle_it4.777
r_scbond_it2.827
r_angle_refined_deg2.768
r_mcangle_it1.934
r_mcbond_it1.029
r_symmetry_hbond_refined0.34
r_nbd_refined0.337
r_symmetry_vdw_refined0.329
r_xyhbond_nbd_refined0.269
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg11.133
r_scangle_it4.777
r_scbond_it2.827
r_angle_refined_deg2.768
r_mcangle_it1.934
r_mcbond_it1.029
r_symmetry_hbond_refined0.34
r_nbd_refined0.337
r_symmetry_vdw_refined0.329
r_xyhbond_nbd_refined0.269
r_chiral_restr0.173
r_bond_refined_d0.028
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17297
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing