2P16

Factor Xa in Complex with the Inhibitor APIXABAN (BMS-562247) AKA 1-(4-METHOXYPHENYL)-7-OXO-6-(4-(2-OXO-1-PIPERIDINYL)PHENYL)-4,5,6,7-TETRAHYDRO-1H-PYRAZOLO[3, 4-C]PYRIDINE-3-CARBOXAMIDE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FJSPDB ENTRY 1FJS WITHOUT INHIBITOR AND SOLVENT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5277200 mM Sodium Acetate, 18% PEG6000, vapor diffusion, hanging drop, temperature 277K, pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.5451.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.4α = 90
b = 72.8β = 90
c = 79.4γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IIC2002-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
12.319.441511627.1

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 1FJS WITHOUT INHIBITOR AND SOLVENT2.319.44150151454485496.80.2320.2290.277RANDOM30
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]
-1.63-1.272.9
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.2
c_scangle_it2.85
c_mcangle_it2.46
c_scbond_it1.9
c_angle_deg1.5
c_mcbond_it1.48
c_improper_angle_d0.76
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.2
c_scangle_it2.85
c_mcangle_it2.46
c_scbond_it1.9
c_angle_deg1.5
c_mcbond_it1.48
c_improper_angle_d0.76
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2238
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms34

Software

Software
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing
CNXrefinement