5WXP

Crystal structure of uPA in complex with upain-2-3-W3A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29850mM sodium citrate, pH 4.6, 2.0M ammonium sulfate supplemented with 5% polyethylene glycol 400
Crystal Properties
Matthews coefficientSolvent content
2.0439.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.821α = 90
b = 120.821β = 90
c = 42.278γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.979SSRFBL17U

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
11.756097.10.06936.43.522375

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 DIFFRACTIONTHROUGHOUT4DVA1.7539.2321226114696.80.2150.2130.249RANDOM39.39
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]
-0.21-0.21-0.210.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.424
r_dihedral_angle_4_deg17.364
r_dihedral_angle_3_deg16.674
r_dihedral_angle_1_deg6.415
r_angle_refined_deg1.219
r_angle_other_deg0.73
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.424
r_dihedral_angle_4_deg17.364
r_dihedral_angle_3_deg16.674
r_dihedral_angle_1_deg6.415
r_angle_refined_deg1.219
r_angle_other_deg0.73
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1984
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms12

Software

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