5YC7

The crystal structure of uPA in complex with 4-Bromobenzylamirne at pH7.4


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% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.1743.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.575α = 90
b = 121.575β = 90
c = 42.212γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2012-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.979SSRFBL17U1

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
129999.50.06132.63.715624
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)
120.503

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 REPLACEMENTTHROUGHOUT4DVA260.791484777799.240.214310.211920.26158RANDOM55.99
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]
0.270.130.27-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.327
r_dihedral_angle_3_deg15.857
r_dihedral_angle_4_deg14.568
r_long_range_B_refined9.281
r_long_range_B_other9.25
r_dihedral_angle_1_deg6.615
r_scangle_other5.459
r_mcangle_it4.481
r_mcangle_other4.48
r_scbond_it3.513
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.327
r_dihedral_angle_3_deg15.857
r_dihedral_angle_4_deg14.568
r_long_range_B_refined9.281
r_long_range_B_other9.25
r_dihedral_angle_1_deg6.615
r_scangle_other5.459
r_mcangle_it4.481
r_mcangle_other4.48
r_scbond_it3.513
r_scbond_other3.498
r_mcbond_it2.905
r_mcbond_other2.895
r_angle_refined_deg1.297
r_angle_other_deg0.889
r_chiral_restr0.08
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1942
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing