4X6I

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 DROP295Lithium sulfate 0.2M, Sodium acetate 0.1M, Peg 8000 30%
Crystal Properties
Matthews coefficientSolvent content
1.8533.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.459α = 90
b = 54.45β = 90
c = 87.87γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352014-01-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54184

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
11.8746.2898.310.25939.969.514804
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)
11.871.93798.160.98157.4

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 REPLACEMENTTHROUGHOUT1ATK1.8746.281406474098.310.18380.1810.237RANDOM8.629
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]
0.26-0.590.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.669
r_dihedral_angle_4_deg16.088
r_dihedral_angle_3_deg13.866
r_dihedral_angle_1_deg6.115
r_angle_refined_deg1.76
r_mcangle_it1.031
r_angle_other_deg0.905
r_mcbond_it0.612
r_mcbond_other0.611
r_chiral_restr0.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.669
r_dihedral_angle_4_deg16.088
r_dihedral_angle_3_deg13.866
r_dihedral_angle_1_deg6.115
r_angle_refined_deg1.76
r_mcangle_it1.031
r_angle_other_deg0.905
r_mcbond_it0.612
r_mcbond_other0.611
r_chiral_restr0.113
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3298
Nucleic Acid Atoms
Solvent Atoms413
Heterogen Atoms96

Software

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