5CT3

The structure of the NK1 fragment of HGF/SF complexed with 2FA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NK1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29319% PEG 4000, 200 mM Na Acetate, 150 mM Tris
Crystal Properties
Matthews coefficientSolvent content
2.2645.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.225α = 90
b = 63.078β = 95.06
c = 57.275γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.981ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
123099.80.0550.05516.13.525692
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)
122.299.80.3983.3

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 REPLACEMENTTHROUGHOUT1NK1226.5124374130399.590.2070.2050.251RANDOM37.006
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]
-0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.012
r_dihedral_angle_4_deg19.113
r_dihedral_angle_3_deg15.801
r_dihedral_angle_1_deg6.421
r_scangle_it4.308
r_mcangle_it3.51
r_scbond_it2.957
r_mcbond_it2.533
r_angle_refined_deg1.235
r_symmetry_hbond_refined0.404
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.012
r_dihedral_angle_4_deg19.113
r_dihedral_angle_3_deg15.801
r_dihedral_angle_1_deg6.421
r_scangle_it4.308
r_mcangle_it3.51
r_scbond_it2.957
r_mcbond_it2.533
r_angle_refined_deg1.235
r_symmetry_hbond_refined0.404
r_nbtor_refined0.302
r_symmetry_vdw_refined0.22
r_nbd_refined0.211
r_xyhbond_nbd_refined0.152
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms2774
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing