2WYJ

Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with monoaryl P4 motifs


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.75CRYSTALLISATION WAS CARRIED OUT USING HANG DROP VAPOUR DIFFUSION METHODS IN 2UL DROPS CONTAINING 1:1 RATIO PROTEIN AND WELL SOLUTION. WELL SOLUTION CONTAINED 16-20% PEG6K, 50MM MES-NAOH (PH5.5-6), 5MM CACL2 AND 50MM NACL, pH 5.75
Crystal Properties
Matthew coefficientSolvent content
1.8332.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.564α = 90
b = 72.485β = 90
c = 78.177γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.383098.20.0622.74.313086
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)
12.382.4996.40.3744

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 1EZQ2.3828.4124236371000.199790.196920.25478RANDOM51.775
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]
-0.86-2.393.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.678
r_dihedral_angle_4_deg15.896
r_dihedral_angle_3_deg11.453
r_scangle_it5.358
r_dihedral_angle_1_deg3.671
r_scbond_it3.469
r_mcangle_it2.741
r_angle_refined_deg1.525
r_mcbond_it1.377
r_chiral_restr0.108
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.678
r_dihedral_angle_4_deg15.896
r_dihedral_angle_3_deg11.453
r_scangle_it5.358
r_dihedral_angle_1_deg3.671
r_scbond_it3.469
r_mcangle_it2.741
r_angle_refined_deg1.525
r_mcbond_it1.377
r_chiral_restr0.108
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_bond_other_d
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_bonded
r_mcbond_other
r_angle_other_deg
r_mcangle_other
r_gen_planes_other
r_scbond_other
r_nbd_refined
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2204
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing