7NXM | pdb_00007nxm

Structure of human cathepsin K in complex with the selective activity-based probe Gu3416

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5TDI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	Composition of reservoir solution was 0.1 M MES/imidazole buffer, containing: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.03 M of each NPS (a mix containing sodium nitrate, disodium hydrogen phosphate and ammonium sulfate) additives, pH 6.5. Morpheus C4 condition

Crystal Properties
Matthews coefficient	Solvent content
1.963	37.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.045	α = 90
b = 71.677	β = 90
c = 80.856	γ = 90

Symmetry
Space Group	P 2 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 300K		2020-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.541870

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.72	50	85.7	0.061	0.079	0.05	0.996	27.18	3.8		17548

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.72	1.75	14.8		0.423	0.598	0.423	0.678	1.4	1.3

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 (All)	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	5TDI	1.72	35.86	17510	895	85.34	0.161	0.1602	0.17	0.1784	0.19	RANDOM	17.819

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]
0.356			-1.202		0.846

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.746
r_dihedral_angle_4_deg	17.225
r_dihedral_angle_other_3_deg	13.112
r_dihedral_angle_3_deg	12.423
r_dihedral_angle_1_deg	5.896
r_lrange_it	5.28
r_lrange_other	5.14
r_scangle_it	3.85
r_scangle_other	3.849
r_scbond_it	2.579
r_scbond_other	2.578
r_mcangle_other	2.38
r_mcangle_it	2.377
r_mcbond_it	1.675
r_mcbond_other	1.661
r_angle_refined_deg	1.633
r_angle_other_deg	1.465
r_symmetry_xyhbond_nbd_refined	0.223
r_nbd_refined	0.209
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.175
r_nbd_other	0.167
r_xyhbond_nbd_refined	0.153
r_symmetry_nbd_refined	0.141
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1652
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing