4AQH

Plasminogen activator inhibitor type-1 in complex with the inhibitor AZ3976


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6PAI-1 WAS CONCENTRATED TO ABOUT 4 G/L IN A BUFFER CONTAINING 10 MM SODIUM ACETATE PH 5.6, 150 MM SODIUM CHLORIDE AND 1 MM EDTA. AZ3976 WAS DISSOLVED IN DEUTERATED DMSO AND ADDED TO THE PROTEIN SAMPLE TO A FINAL CONCENTRATION OF 0.3 MM. CRYSTALS WERE OBTAINED BY THE HANGING DROP VAPOR DIFFUSION TECHNIQUE: 2.5 UL PROTEIN SAMPLE WAS MIXED WITH 1 UL OF A WELL SOLUTION CONTAINING 2.0 M SODIUM CHLORIDE, 100 MM BIS-TRIS PH 6.8
Crystal Properties
Matthews coefficientSolvent content
3.261

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.399α = 90
b = 119.399β = 90
c = 99.691γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.449.91000.1165.9621792
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)
12.42.461000.72.45.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1DVN2.460.0158169316398.670.158670.157430.18138RANDOM45.905
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]
4.454.45-8.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.198
r_dihedral_angle_4_deg19.41
r_dihedral_angle_3_deg17.641
r_dihedral_angle_1_deg5.464
r_scangle_it3.793
r_scbond_it2.358
r_mcangle_it1.564
r_angle_refined_deg1.485
r_mcbond_it0.826
r_chiral_restr0.099
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.198
r_dihedral_angle_4_deg19.41
r_dihedral_angle_3_deg17.641
r_dihedral_angle_1_deg5.464
r_scangle_it3.793
r_scbond_it2.358
r_mcangle_it1.564
r_angle_refined_deg1.485
r_mcbond_it0.826
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.007
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_mcangle_other
r_scbond_other
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 Atoms9115
Nucleic Acid Atoms
Solvent Atoms244
Heterogen Atoms69

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing