1GMN

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% PEG8000, 8% ETHYLENE GLYCOL, 0.55M SODIUM DIHYDROGEN PHOSPHATE 0.10M SODIUM HEPES, PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.2144

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.56α = 90
b = 86.56β = 90
c = 117.75γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2000-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.1SRSPX14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.32199.50.07710.51320349353.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.35990.375

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 1BHT2.3211958095195.90.2620.2620.279RANDOM57.4
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]
-7.98-7.9815.97
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.6
c_scangle_it3.39
c_mcangle_it2.94
c_scbond_it2.27
c_mcbond_it1.7
c_angle_deg1.2
c_improper_angle_d0.77
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.6
c_scangle_it3.39
c_mcangle_it2.94
c_scbond_it2.27
c_mcbond_it1.7
c_angle_deg1.2
c_improper_angle_d0.77
c_bond_d0.007
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 Atoms2170
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms116

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing