5COE

The structure of the NK1 fragment of HGF/SF complexed with HEPES


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
2.2745.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.282α = 90
b = 63.081β = 95.04
c = 57.381γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-10-30MSINGLE 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
12.185099.60.0540.05414.63.419668
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)
12.182.2597.70.3742.8

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 REPLACEMENTTHROUGHOUT1NK12.1840.6118649100798.960.210.2070.264RANDOM44.266
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]
-0.01-0.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.774
r_dihedral_angle_4_deg17.809
r_dihedral_angle_3_deg16.895
r_dihedral_angle_1_deg6.617
r_scangle_it5.188
r_mcangle_it3.988
r_scbond_it3.565
r_mcbond_it2.805
r_angle_refined_deg1.376
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.774
r_dihedral_angle_4_deg17.809
r_dihedral_angle_3_deg16.895
r_dihedral_angle_1_deg6.617
r_scangle_it5.188
r_mcangle_it3.988
r_scbond_it3.565
r_mcbond_it2.805
r_angle_refined_deg1.376
r_chiral_restr0.095
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_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 Atoms137
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing