4H42

Synthesis of a Weak Basic uPA Inhibitor and Crystal Structure of Complex with uPA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62982.0 M ammonium sulfate, 50 mM sodium citrate pH 4.6 and 5% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1642.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.916α = 90
b = 120.916β = 90
c = 42.875γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 60002011-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.0160.4679.021558112312
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.012.2495.377.734.68

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.0160.4611690620790.2110.2070.285RANDOM20.93
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]
-0.13-0.13-0.130.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.736
r_dihedral_angle_3_deg18.482
r_dihedral_angle_4_deg16.445
r_dihedral_angle_1_deg7.754
r_scangle_it4.242
r_scbond_it2.654
r_angle_refined_deg2.01
r_mcangle_it1.748
r_mcbond_it0.969
r_angle_other_deg0.922
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.736
r_dihedral_angle_3_deg18.482
r_dihedral_angle_4_deg16.445
r_dihedral_angle_1_deg7.754
r_scangle_it4.242
r_scbond_it2.654
r_angle_refined_deg2.01
r_mcangle_it1.748
r_mcbond_it0.969
r_angle_other_deg0.922
r_chiral_restr0.102
r_bond_refined_d0.016
r_gen_planes_refined0.009
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1952
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms27

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
REFMACrefinement