4X6J

Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ATK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP295Potassium chloride 0.2M, HEPES 0.05M, 5/4 PO/OH 35%
Crystal Properties
Matthews coefficientSolvent content
2.0539.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.219α = 90
b = 44.403β = 116.42
c = 51.354γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352014-01-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.58545.9997.530.085340.9919.121.925360
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.5851.64290.011.1240.1891.171.8

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 REPLACEMENTTHROUGHOUT1ATK1.5945.9949603124697.430.18590.18320.2376RANDOM18.432
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]
0.410.51-0.6-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.795
r_dihedral_angle_3_deg14.68
r_dihedral_angle_4_deg12.253
r_dihedral_angle_1_deg6.428
r_mcangle_it2.113
r_angle_refined_deg1.925
r_mcbond_it1.493
r_mcbond_other1.49
r_angle_other_deg1.458
r_chiral_restr0.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.795
r_dihedral_angle_3_deg14.68
r_dihedral_angle_4_deg12.253
r_dihedral_angle_1_deg6.428
r_mcangle_it2.113
r_angle_refined_deg1.925
r_mcbond_it1.493
r_mcbond_other1.49
r_angle_other_deg1.458
r_chiral_restr0.112
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1649
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PROTEUM PLUSdata reduction