4D3C

Crystal structure of the NK1 domain of HGF in complex with anti-HGF monoclonal antibody SFN68.


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
3.3363.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.703α = 90
b = 297.692β = 90
c = 70.713γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93.15CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLSPAL/PLS

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
12.6229.7995.50.074.5255411.5

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 1JPT, 1NK1.2.6229.7925541134795.510.269130.26760.2975885.704
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]
1.12-0.01-1.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.49
r_dihedral_angle_4_deg15.611
r_dihedral_angle_3_deg15.563
r_dihedral_angle_1_deg6.15
r_angle_refined_deg1.456
r_angle_other_deg0.835
r_chiral_restr0.073
r_bond_refined_d0.012
r_bond_other_d0.007
r_gen_planes_refined0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.49
r_dihedral_angle_4_deg15.611
r_dihedral_angle_3_deg15.563
r_dihedral_angle_1_deg6.15
r_angle_refined_deg1.456
r_angle_other_deg0.835
r_chiral_restr0.073
r_bond_refined_d0.012
r_bond_other_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.002
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
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 Atoms4225
Nucleic Acid Atoms
Solvent Atoms22
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling