1WAY

Active site thrombin inhibitors


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QJ1PDB ENTRY 1QJ1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.3PH 7.30
Crystal Properties
Matthews coefficientSolvent content
2.5451.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.503α = 90
b = 71.512β = 100.46
c = 72.205γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU CCDCONFOCAL MULTILAYER2002-11-06MSINGLE 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
127197.70.072.71.923016
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)
12.022.0799.10.3231.9

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 1QJ12.0249.78214281135980.1610.1580.231RANDOM18.37
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]
0.65-0.54-0.55-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.917
r_dihedral_angle_4_deg16.74
r_dihedral_angle_3_deg13.724
r_dihedral_angle_1_deg6.458
r_scangle_it4.897
r_scbond_it3.699
r_mcangle_it3.561
r_mcbond_it3.235
r_angle_refined_deg1.458
r_angle_other_deg0.808
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.917
r_dihedral_angle_4_deg16.74
r_dihedral_angle_3_deg13.724
r_dihedral_angle_1_deg6.458
r_scangle_it4.897
r_scbond_it3.699
r_mcangle_it3.561
r_mcbond_it3.235
r_angle_refined_deg1.458
r_angle_other_deg0.808
r_symmetry_vdw_other0.307
r_nbd_refined0.223
r_symmetry_hbond_refined0.204
r_nbd_other0.188
r_nbtor_refined0.182
r_xyhbond_nbd_refined0.174
r_chiral_restr0.089
r_nbtor_other0.083
r_symmetry_vdw_refined0.067
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.005
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 Atoms2356
Nucleic Acid Atoms
Solvent Atoms391
Heterogen Atoms30

Software

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