3QN7

Potent and selective bicyclic peptide inhibitor (UK18) of human urokinase-type plasminogen activator(uPA)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NWN2NWN.pdb

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.32932M ammonium sulfate, 0.05M sodium citrate, 5%(v/v) PEG 400, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
238.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.25α = 90
b = 121.25β = 90
c = 42.72γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rToroidal focusing mirrors2010-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.939ESRFID14-4

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
11.939.5799.80.07912.25.41815518155
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)
11.921000.4053.95.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2NWN.pdb1.939.57181551748794699.760.198220.198220.195270.25233RANDOM34.287
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]
-0.96-0.48-0.961.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.911
r_dihedral_angle_4_deg19.594
r_dihedral_angle_3_deg16.772
r_dihedral_angle_1_deg7.462
r_scangle_it4.94
r_scbond_it3.22
r_mcangle_it2.344
r_angle_refined_deg1.9
r_mcbond_it1.329
r_chiral_restr0.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.911
r_dihedral_angle_4_deg19.594
r_dihedral_angle_3_deg16.772
r_dihedral_angle_1_deg7.462
r_scangle_it4.94
r_scbond_it3.22
r_mcangle_it2.344
r_angle_refined_deg1.9
r_mcbond_it1.329
r_chiral_restr0.154
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2050
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms9

Software

Software
Software NamePurpose
ADSCdata collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling