2C8Y

thrombin inhibitors


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.3PH 7.30
Crystal Properties
Matthews coefficientSolvent content
2.3847.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.731α = 90
b = 71.516β = 100.51
c = 72.422γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU CCDCONFOCAL MULTILAYERMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
12.229.2299.70.135.32.9118049
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)
12.22.2899.10.442.22.82

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 1QJ12.229.221713291699.70.1880.1850.259RANDOM26.73
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]
0.5-1.52-0.45-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.338
r_dihedral_angle_4_deg17.283
r_dihedral_angle_3_deg14.239
r_dihedral_angle_1_deg6.375
r_angle_refined_deg1.386
r_angle_other_deg0.855
r_symmetry_vdw_other0.258
r_nbd_refined0.202
r_nbd_other0.192
r_nbtor_refined0.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.338
r_dihedral_angle_4_deg17.283
r_dihedral_angle_3_deg14.239
r_dihedral_angle_1_deg6.375
r_angle_refined_deg1.386
r_angle_other_deg0.855
r_symmetry_vdw_other0.258
r_nbd_refined0.202
r_nbd_other0.192
r_nbtor_refined0.183
r_symmetry_hbond_refined0.139
r_xyhbond_nbd_refined0.106
r_scangle_it0.099
r_chiral_restr0.085
r_scbond_it0.083
r_nbtor_other0.082
r_mcangle_it0.08
r_symmetry_vdw_refined0.063
r_mcbond_it0.058
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2362
Nucleic Acid Atoms
Solvent Atoms298
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
IN-HOUSEphasing