4TY6

Factor XIa in complex with the inhibitor 4-{2-[(1S)-1-({[trans-4-(aminomethyl)cyclohexyl]carbonyl}amino)-2-phenylethyl]-1H-imidazol-4-yl}benzamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherfactor XIa

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6277100 MM SODIUM ACETATE, PH 4.6, 26%(w/v) MEPEG2000, 200 MM AMMONIUM SULFATE
Crystal Properties
Matthews coefficientSolvent content
3.5164.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.3α = 90
b = 79.3β = 90
c = 106.6γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

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
11.855095.80.07719.863236021.59
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)
11.851.9277.60.3783.33.3

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 MUTANT1.8542.1132278106695.890.17040.16940.2006RANDOM25.76
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]
-3.2375-3.23756.4751
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion14.42
t_omega_torsion3.99
t_angle_deg1
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_torsion14.42
t_omega_torsion3.99
t_angle_deg1
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 Atoms1903
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms70

Software

Software
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
Cootmodel building
BUSTERrefinement
AMoREphasing