6AG3

Crystal structure of uPA in complex with 3,5-bis(azanyl)-N-carbamimidoyl-6-(2,4-dimethoxypyrimidin-5-yl)pyrazine-2-carboxamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DVA 

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
2.1542.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.892α = 90
b = 120.892β = 90
c = 42.268γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNFPSS BEAMLINE BL19U10.979NFPSSBL19U1

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
12.4860.4599.10.14217.34.88040
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)
12.52.540.558

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 REPLACEMENTTHROUGHOUT4DVA2.4860.45762042098.80.20.1960.267RANDOM47.81
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]
-1.45-0.72-1.454.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.246
r_dihedral_angle_3_deg16.975
r_dihedral_angle_4_deg14.947
r_dihedral_angle_1_deg8.383
r_long_range_B_refined7.864
r_scangle_other5.292
r_mcangle_it4.775
r_mcangle_other4.773
r_scbond_it3.293
r_scbond_other3.291
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.246
r_dihedral_angle_3_deg16.975
r_dihedral_angle_4_deg14.947
r_dihedral_angle_1_deg8.383
r_long_range_B_refined7.864
r_scangle_other5.292
r_mcangle_it4.775
r_mcangle_other4.773
r_scbond_it3.293
r_scbond_other3.291
r_mcbond_other2.995
r_mcbond_it2.994
r_angle_refined_deg1.632
r_angle_other_deg0.965
r_chiral_restr0.09
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
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 Atoms1933
Nucleic Acid Atoms
Solvent Atoms14
Heterogen Atoms24

Software

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