1R1W

CRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF THE HEPATOCYTE GROWTH FACTOR RECEPTOR C-MET


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R0Ppdb entry 1r0p

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.1277PEG 5000 MME, isopropanol, Hepes, pH 7.10, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2244.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.038α = 90
b = 46.028β = 90
c = 158.448γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2002-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
11.83095.70.08419.65.928705
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)
1.81.8690.40.3154.52644

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1r0p1.8302870527250140595.580.174470.174470.172970.20381RANDOM18.291
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]
0.03-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.514
r_scangle_it3.238
r_scbond_it1.959
r_angle_refined_deg1.29
r_mcangle_it1.272
r_angle_other_deg0.805
r_mcbond_it0.671
r_symmetry_vdw_other0.298
r_nbd_refined0.244
r_symmetry_vdw_refined0.238
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.514
r_scangle_it3.238
r_scbond_it1.959
r_angle_refined_deg1.29
r_mcangle_it1.272
r_angle_other_deg0.805
r_mcbond_it0.671
r_symmetry_vdw_other0.298
r_nbd_refined0.244
r_symmetry_vdw_refined0.238
r_nbd_other0.237
r_symmetry_hbond_refined0.222
r_xyhbond_nbd_refined0.126
r_nbtor_other0.082
r_chiral_restr0.076
r_bond_refined_d0.011
r_gen_planes_other0.008
r_gen_planes_refined0.007
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2286
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms

Software

Software
Software NamePurpose
ProDCdata collection
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement