3B23

Crystal structure of thrombin-variegin complex: Insights of a novel mechanism of inhibition and design of tunable thrombin inhibitors


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ABIPDB ENTRY 1ABI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.4277100mM HEPES buffer pH 7.4, 20-25% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5752.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.658α = 90
b = 50.826β = 98.7
c = 61.535γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2007-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9795NSLSX29A

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
12.45098.10.053203.615137-3
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)
12.42.46970.1545.43.1

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 1ABI2.4301329872492.820.210490.207870.25944RANDOM57.826
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]
-1.05-4.792.49-2.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.426
r_dihedral_angle_4_deg19.229
r_dihedral_angle_3_deg14.327
r_dihedral_angle_1_deg6.818
r_scangle_it1.936
r_angle_refined_deg1.224
r_scbond_it1.191
r_mcangle_it0.931
r_angle_other_deg0.811
r_mcbond_it0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.426
r_dihedral_angle_4_deg19.229
r_dihedral_angle_3_deg14.327
r_dihedral_angle_1_deg6.818
r_scangle_it1.936
r_angle_refined_deg1.224
r_scbond_it1.191
r_mcangle_it0.931
r_angle_other_deg0.811
r_mcbond_it0.49
r_mcbond_other0.078
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2464
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling