1GP9

A New Crystal Form of the Nk1 Splice Variant of Hgf/Sf Demonstrates Extensive Hinge Movement and Suggests that the Nk1 Dimer Originates by Domain Swapping


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NK1PDB ENTRIES 1NK1 1BHT
experimental modelPDB 1BHTPDB ENTRIES 1NK1 1BHT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.518% PEG4000, 10% 2-PROPANOL, 0.1M SODIUM HEPES, PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.48α = 90
b = 78.26β = 90
c = 304.46γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH1998-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX7.2SRSPX7.2

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
12.443092.20.0451212.833095352.6
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)
12.442.595.80.352

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 ENTRIES 1NK1 1BHT2.519.9228444142092.10.2370.2370.288RANDOM58.5
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]
-5.837.59-1.76
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.5
c_scangle_it6.36
c_mcangle_it5.25
c_scbond_it4.6
c_mcbond_it3.41
c_angle_deg1.7
c_improper_angle_d1.06
c_bond_d0.011
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.5
c_scangle_it6.36
c_mcangle_it5.25
c_scbond_it4.6
c_mcbond_it3.41
c_angle_deg1.7
c_improper_angle_d1.06
c_bond_d0.011
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5467
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms75

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing