4NA8

Factor XIa in complex with the inhibitor 5-aminocarbonyl-2-[3-[(2s,4r)-6-carbamimidoyl-4-methyl-4-phenyl-2,3-dihydro-1h-quinolin-2-yl]phenyl]benzoic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherfactor XIa

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6277100 mM sodium acetate, pH 4.6, 26% (w/v) MEPEG2000, 200 mM ammonium sulfate, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.5965.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.05α = 90
b = 79.05β = 90
c = 106.91γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 92MICROMAX CONFOCAL2003-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54180

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
12.3106.997.80.11421.210.51729232.26
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)
12.32.4398.40.349710.7

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 REPLACEMENTTHROUGHOUTFACTOR XIA DOUBLE MUTANT2.334.231630439092.280.23050.22950.2708RANDOM22.1813
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]
-3.2542-3.25426.5084
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion17.36
t_omega_torsion3.37
t_angle_deg1.16
t_bond_d0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion17.36
t_omega_torsion3.37
t_angle_deg1.16
t_bond_d0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1860
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms51

Software

Software
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
AMoREphasing
BUSTERrefinement