4BVC

Identification of small molecule inhibitors selective for apo(a) kringles KIV-7, KIV-10 and KV.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.58% PEG8000, 0.1M TRIS PH8.5, 0.2M LISO4
Crystal Properties
Matthews coefficientSolvent content
1.728

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 24.55α = 90
b = 45.69β = 90
c = 55.11γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU CCD-A200-CUMIRRORS2012-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+

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
11.624.6930.09135.980062
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)
11.61.64570.491.72.7

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 3KIV1.623.61736636589.290.158790.157060.19419RANDOM11.817
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]
0.05-0.40.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.505
r_dihedral_angle_3_deg13.145
r_dihedral_angle_4_deg7.421
r_dihedral_angle_1_deg5.808
r_angle_other_deg3.654
r_angle_refined_deg1.714
r_chiral_restr0.079
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_gen_planes_other0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.505
r_dihedral_angle_3_deg13.145
r_dihedral_angle_4_deg7.421
r_dihedral_angle_1_deg5.808
r_angle_other_deg3.654
r_angle_refined_deg1.714
r_chiral_restr0.079
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_gen_planes_other0.005
r_bond_other_d
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms638
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing