3N3G

4-(3-Trifluoromethylphenyl)-pyrimidine-2-carbonitrile as cathepsin S inhibitors: N3, not N1 is critically important


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5298crystallisation solution: 50 mM NaAcetate, 0.25 M NaCl, 4 mM MMTS, 30% PEG 4K, 0.1 M NaCitrate, 0,2 M (NH4)2SO4, 10 mM DMSO, 10 mM DTT. Cryoprotectant composition: 30% PEG 4K, 0.1 M NaCitrate, 0.2 M (NH4)2SO4, 15% PEG 400 (+ 10% compound). Ligand was introduced by soaking crystals prepared with another compound, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8957.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.757α = 90
b = 85.757β = 90
c = 150.902γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATERIGAKU RAXIS IV2007-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.685.7587.70.1665.35.2865361
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)
1.61.6624.90.5011.11.411825

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 REPLACEMENTTHROUGHOUT1.674.5665283328987.780.2250.2230.264RANDOM24.555
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]
-0.03-0.030.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.388
r_dihedral_angle_4_deg24.167
r_dihedral_angle_3_deg11.873
r_dihedral_angle_1_deg5.591
r_scangle_it1.971
r_scbond_it1.347
r_angle_refined_deg1.145
r_angle_other_deg0.871
r_mcangle_it0.839
r_mcbond_it0.553
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.388
r_dihedral_angle_4_deg24.167
r_dihedral_angle_3_deg11.873
r_dihedral_angle_1_deg5.591
r_scangle_it1.971
r_scbond_it1.347
r_angle_refined_deg1.145
r_angle_other_deg0.871
r_mcangle_it0.839
r_mcbond_it0.553
r_symmetry_vdw_other0.25
r_symmetry_vdw_refined0.214
r_nbd_refined0.19
r_nbd_other0.189
r_nbtor_refined0.18
r_symmetry_hbond_refined0.167
r_xyhbond_nbd_refined0.144
r_mcbond_other0.104
r_nbtor_other0.085
r_chiral_restr0.062
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3372
Nucleic Acid Atoms
Solvent Atoms512
Heterogen Atoms100

Software

Software
Software NamePurpose
d*TREKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction