1GMO

CRYSTAL STRUCTURES OF NK1-HEPARIN COMPLEXES REVEAL THE BASIS FOR NK1 ACTIVITY AND ENABLE ENGINEERING OF POTENT AGONISTS OF THE MET RECEPTOR


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.510% PEG4000, 8% ETHYLENE GLYCOL, 0.10M SODIUM PARA-TOLUENE SULFONATE,0.10M SODIUM HEPES, PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.4349

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 179.7α = 90
b = 174.1β = 90
c = 59.9γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2000-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.2SRSPX14.2

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
12.952095.20.06312637651378.3
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)
12.953.0291.40.327

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 AND 1BHT32036626182495.30.2540.2540.295RANDOM60.4
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]
-4.31.023.28
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.7
c_scangle_it2.68
c_mcangle_it2.55
c_scbond_it1.67
c_mcbond_it1.42
c_angle_deg1.3
c_improper_angle_d0.87
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.7
c_scangle_it2.68
c_mcangle_it2.55
c_scbond_it1.67
c_mcbond_it1.42
c_angle_deg1.3
c_improper_angle_d0.87
c_bond_d0.009
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 Atoms10477
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms895

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing