1V7M

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
2.2945.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.099α = 90
b = 46.771β = 90.48
c = 185.151γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH1999-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

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
12.560920.0748.12.636766-148.9
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)
2.52.59710.3181.11.62814

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 1IAI2.5145.2834911185292.870.231850.227510.31579RANDOM49.886
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]
-0.080.480.050.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.937
r_scangle_it3.767
r_scbond_it2.343
r_angle_refined_deg2.008
r_mcangle_it1.635
r_mcbond_it0.871
r_symmetry_vdw_refined0.286
r_nbd_refined0.272
r_xyhbond_nbd_refined0.22
r_symmetry_hbond_refined0.186
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.937
r_scangle_it3.767
r_scbond_it2.343
r_angle_refined_deg2.008
r_mcangle_it1.635
r_mcbond_it0.871
r_symmetry_vdw_refined0.286
r_nbd_refined0.272
r_xyhbond_nbd_refined0.22
r_symmetry_hbond_refined0.186
r_chiral_restr0.126
r_bond_refined_d0.02
r_gen_planes_refined0.007
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 Atoms8746
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing