2I9B

Crystal structure of ATF-urokinase receptor complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529322.5% w/v PEG3350, 200 mM ammonium sulfate, 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8256.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.914α = 90
b = 281.921β = 105.41
c = 62.811γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 225 mm2005-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0000APS22-BM

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
12.85091.20.04617.62.84704847048-3
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)
12.82.951.30.2062.441.82636

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 ENTRY 1YWH, 2I9A2.81544793191191.180.223720.221940.26498RANDOM67.301
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]
3.82.52-3.91.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.459
r_scangle_it18.474
r_scbond_it15.956
r_dihedral_angle_3_deg14.196
r_mcangle_it12.726
r_dihedral_angle_4_deg12.344
r_mcbond_it9.938
r_dihedral_angle_1_deg2.877
r_angle_refined_deg1.888
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.459
r_scangle_it18.474
r_scbond_it15.956
r_dihedral_angle_3_deg14.196
r_mcangle_it12.726
r_dihedral_angle_4_deg12.344
r_mcbond_it9.938
r_dihedral_angle_1_deg2.877
r_angle_refined_deg1.888
r_nbtor_refined0.314
r_symmetry_hbond_refined0.272
r_nbd_refined0.239
r_xyhbond_nbd_refined0.208
r_symmetry_vdw_refined0.179
r_chiral_restr0.131
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11696
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing