4X6J | pdb_00004x6j

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ATK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	Potassium chloride 0.2M, HEPES 0.05M, 5/4 PO/OH 35%

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.99

Crystal Data

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

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	Bruker Platinum 135		2014-01-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.585	45.99	97.53	0.08534	0.991	9.12	1.9		25360

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)	Redundancy	Number Unique Reflections (All)
1	1.585	1.642	90.01		1.124	0.189	1.17	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1ATK	1.59	45.99	49603	1246	97.43	0.1859	0.1832	0.19	0.2376	0.24	RANDOM	18.432

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]
0.41		0.51	-0.6		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.795
r_dihedral_angle_3_deg	14.68
r_dihedral_angle_4_deg	12.253
r_dihedral_angle_1_deg	6.428
r_mcangle_it	2.113
r_angle_refined_deg	1.925
r_mcbond_it	1.493
r_mcbond_other	1.49
r_angle_other_deg	1.458
r_chiral_restr	0.112

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.795
r_dihedral_angle_3_deg	14.68
r_dihedral_angle_4_deg	12.253
r_dihedral_angle_1_deg	6.428
r_mcangle_it	2.113
r_angle_refined_deg	1.925
r_mcbond_it	1.493
r_mcbond_other	1.49
r_angle_other_deg	1.458
r_chiral_restr	0.112
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1649
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.