3HPT

Crystal structure of human FxA in complex with (S)-2-cyano-1-(2-methylbenzofuran-5-yl)-3-(2-oxo-1-(2-oxo-2-(pyrrolidin-1-yl)ethyl)azepan-3-yl)guanidine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629815-22% w/v PEG MME 5000, 0.01 M Calcium acetate, 0.35 M Sodium acetate, 0.1 M Lithium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3647.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.98α = 90
b = 78.66β = 102.49
c = 73.67γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IICOsmic mirrors1999-01-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54178

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
12.195099.80.08514.84.335677
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)
12.192.2899.90.4382.63.3

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 REPLACEMENTTHROUGHOUT2.195033872178199.380.178860.175670.23868RANDOM33.605
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]
0.78-0.59-0.05-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.078
r_dihedral_angle_4_deg19.278
r_dihedral_angle_3_deg15.079
r_dihedral_angle_1_deg5.831
r_scangle_it2.544
r_scbond_it1.541
r_angle_refined_deg1.326
r_mcangle_it1.236
r_mcbond_it0.662
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.078
r_dihedral_angle_4_deg19.278
r_dihedral_angle_3_deg15.079
r_dihedral_angle_1_deg5.831
r_scangle_it2.544
r_scbond_it1.541
r_angle_refined_deg1.326
r_mcangle_it1.236
r_mcbond_it0.662
r_nbtor_refined0.3
r_nbd_refined0.205
r_symmetry_vdw_refined0.183
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.149
r_metal_ion_refined0.121
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms4915
Nucleic Acid Atoms
Solvent Atoms554
Heterogen Atoms162

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling