5YC6

The crystal structure of uPA in complex with 4-Bromobenzylamirne at pH4.6


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
2.1643.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.853α = 90
b = 120.853β = 90
c = 42.627γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2013-04-08MSINGLE 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
11.135097.80.08329.53.673602
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)
11.130.45

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 REPLACEMENTTHROUGHOUT4DVA1.185069904369595.90.1980.1970.228RANDOM18.26
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]
-0.1-0.05-0.10.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.037
r_sphericity_free17.309
r_dihedral_angle_4_deg16
r_dihedral_angle_3_deg14.108
r_dihedral_angle_1_deg6.596
r_rigid_bond_restr5.765
r_sphericity_bonded4.575
r_long_range_B_refined2.075
r_long_range_B_other2.074
r_angle_refined_deg1.405
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.037
r_sphericity_free17.309
r_dihedral_angle_4_deg16
r_dihedral_angle_3_deg14.108
r_dihedral_angle_1_deg6.596
r_rigid_bond_restr5.765
r_sphericity_bonded4.575
r_long_range_B_refined2.075
r_long_range_B_other2.074
r_angle_refined_deg1.405
r_scangle_other1.199
r_scbond_it1.114
r_scbond_other1.111
r_mcangle_it1.094
r_mcangle_other1.094
r_angle_other_deg0.929
r_mcbond_it0.887
r_mcbond_other0.884
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.003
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1942
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing