1WU1

Factor Xa in complex with the inhibitor 4-[(5-chloroindol-2-yl)sulfonyl]-2-(2-methylpropyl)-1-[[5-(pyridin-4-yl) pyrimidin-2-yl]carbonyl]piperazine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5293PEG6000, NaAcetate, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.244.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.569α = 90
b = 72.487β = 90
c = 79.02γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATERIGAKU RAXIS IIC1999-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.542

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.339.5190.60.0640.33811.72.913656
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3884.30.3380.3382.892.89

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 DIFFRACTIONRIGID BODY REFINEMENTTHROUGHOUT1FAX2.325129336971000.19130.188710.23535RANDOM45.3
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]
0.31-1.71.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.164
r_dihedral_angle_4_deg30.158
r_dihedral_angle_3_deg18.214
r_dihedral_angle_1_deg7.279
r_scangle_it3.961
r_mcangle_it3.175
r_scbond_it2.648
r_angle_refined_deg2.116
r_mcbond_it1.93
r_nbtor_refined0.328
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.164
r_dihedral_angle_4_deg30.158
r_dihedral_angle_3_deg18.214
r_dihedral_angle_1_deg7.279
r_scangle_it3.961
r_mcangle_it3.175
r_scbond_it2.648
r_angle_refined_deg2.116
r_mcbond_it1.93
r_nbtor_refined0.328
r_nbd_refined0.25
r_metal_ion_refined0.215
r_symmetry_vdw_refined0.211
r_xyhbond_nbd_refined0.183
r_symmetry_hbond_refined0.149
r_chiral_restr0.13
r_bond_refined_d0.022
r_gen_planes_refined0.008
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2155
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms35

Software

Software
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
REFMACrefinement