3BT1

Structure of urokinase receptor, urokinase and vitronectin complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FD6PDB ENTRY 2FD6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS7.529512% PEG 3350, 50mM HEPES pH 7.5, MICRODIALYSIS, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.7555.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.353α = 90
b = 105.187β = 90
c = 55.36γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.810099.50.0810.08133.15.91454082
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.91000.8030.8032.65.9

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 2FD62.827.681377872699.60.2440.2410.308RANDOM54.32
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]
0.48-3.252.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.371
r_dihedral_angle_3_deg21.248
r_dihedral_angle_4_deg19.56
r_dihedral_angle_1_deg9.464
r_scangle_it2.154
r_angle_refined_deg1.821
r_scbond_it1.356
r_angle_other_deg1.048
r_mcangle_it0.958
r_mcbond_it0.746
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.371
r_dihedral_angle_3_deg21.248
r_dihedral_angle_4_deg19.56
r_dihedral_angle_1_deg9.464
r_scangle_it2.154
r_angle_refined_deg1.821
r_scbond_it1.356
r_angle_other_deg1.048
r_mcangle_it0.958
r_mcbond_it0.746
r_nbd_refined0.266
r_symmetry_vdw_other0.246
r_nbd_other0.221
r_xyhbond_nbd_refined0.196
r_nbtor_refined0.191
r_symmetry_vdw_refined0.185
r_xyhbond_nbd_other0.163
r_mcbond_other0.105
r_chiral_restr0.102
r_nbtor_other0.1
r_symmetry_hbond_refined0.064
r_bond_refined_d0.016
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3394
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing