3D66

Crystal structure of Thrombin-Activatable Fibrinolysis Inhibitor (TAFI)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION627716-18% PEG 3000, 0.18-0.22mM Na/K-tartrate, 50mM L-glutamate, 50 mM L-arginine, pH 6.0, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.6165.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 161.74α = 90
b = 161.74β = 90
c = 139.45γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.26206ESRFID29

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
13.149.511000.10513.98.63862138593-3.7
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)
13.13.271000.8332.68.7

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1KWM3.149.513663836638195399.990.206210.204420.24038RANDOM80.939
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]
3.981.993.98-5.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.063
r_dihedral_angle_3_deg17.734
r_dihedral_angle_4_deg17.174
r_dihedral_angle_1_deg10.449
r_scangle_it2.369
r_angle_refined_deg1.751
r_scbond_it1.58
r_mcangle_it1.198
r_angle_other_deg1.099
r_mcbond_it0.959
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.063
r_dihedral_angle_3_deg17.734
r_dihedral_angle_4_deg17.174
r_dihedral_angle_1_deg10.449
r_scangle_it2.369
r_angle_refined_deg1.751
r_scbond_it1.58
r_mcangle_it1.198
r_angle_other_deg1.099
r_mcbond_it0.959
r_symmetry_vdw_other0.342
r_symmetry_vdw_refined0.31
r_nbd_refined0.246
r_symmetry_hbond_refined0.225
r_nbd_other0.21
r_xyhbond_nbd_refined0.208
r_nbtor_refined0.204
r_mcbond_other0.126
r_xyhbond_nbd_other0.102
r_chiral_restr0.098
r_nbtor_other0.094
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.003
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9735
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms129

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
SCALAdata scaling
PHASERphasing