4FWW

Crystal structure of the Sema-PSI extracellular domains of human RON receptor tyrosine kinase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2UZXPDB entry 2UZX chain B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.629819% PEG 4000, 0.1 M Sodium Acetate, pH 4.6, 0.2 M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0359.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.4α = 90
b = 73.3β = 97.4
c = 87.9γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDMARMOSAIC 300 mm CCDmirrors2010-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0332APS23-ID-B

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
11.8519.32900.06910.462.85726951510-3
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)
11.851.963.70.441.472

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2UZX chain B1.8519.325151048882262789.950.193110.190910.23245RANDOM51.634
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.483
r_dihedral_angle_4_deg20.998
r_dihedral_angle_3_deg15.249
r_dihedral_angle_1_deg8.048
r_scangle_it4.159
r_scbond_it2.72
r_mcangle_it1.69
r_angle_refined_deg1.548
r_mcbond_it1.032
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.483
r_dihedral_angle_4_deg20.998
r_dihedral_angle_3_deg15.249
r_dihedral_angle_1_deg8.048
r_scangle_it4.159
r_scbond_it2.72
r_mcangle_it1.69
r_angle_refined_deg1.548
r_mcbond_it1.032
r_nbtor_refined0.315
r_symmetry_hbond_refined0.307
r_nbd_refined0.231
r_symmetry_vdw_refined0.211
r_xyhbond_nbd_refined0.192
r_chiral_restr0.125
r_gen_planes_refined0.013
r_bond_refined_d0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3845
Nucleic Acid Atoms
Solvent Atoms358
Heterogen Atoms127

Software

Software
Software NamePurpose
JBluIce-EPICSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling