3TK6

factor Xa in complex with D46-5241


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5293pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5151.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.466α = 90
b = 72.412β = 90
c = 79.074γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IICconfocal mirror2004-12-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.836.299.40.04215.73.11305333053327
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)
11.81.86990.3353.12.862999

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 REPLACEMENTTHROUGHOUT1.8252905214721000.204820.202920.24114RANDOM30.727
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]
0.8-1.130.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.326
r_dihedral_angle_4_deg18.532
r_dihedral_angle_3_deg13.753
r_dihedral_angle_1_deg6.301
r_scangle_it2.604
r_mcangle_it2.186
r_scbond_it1.761
r_angle_refined_deg1.547
r_mcbond_it1.328
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.326
r_dihedral_angle_4_deg18.532
r_dihedral_angle_3_deg13.753
r_dihedral_angle_1_deg6.301
r_scangle_it2.604
r_mcangle_it2.186
r_scbond_it1.761
r_angle_refined_deg1.547
r_mcbond_it1.328
r_nbtor_refined0.312
r_nbd_refined0.207
r_symmetry_vdw_refined0.162
r_xyhbond_nbd_refined0.16
r_metal_ion_refined0.16
r_symmetry_hbond_refined0.124
r_chiral_restr0.114
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms2185
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms31

Software

Software
Software NamePurpose
manufacturerdata collection
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
REFMACphasing