7NXL | pdb_00007nxl

Structure of human cathepsin K in complex with the acrylamide inhibitor Gu3110

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7NXM	D_1292114281

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
1.98	38.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.366	α = 90
b = 71.819	β = 90
c = 80.771	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		2020-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	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	40.39	93	0.14	0.168	0.093	0.996	20.94	5.6		19606

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	95.3		1.495	0.941	0.469		3.6

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-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	FREE R-VALUE	D_1292114281	1.8	35.226	18051	910	99.575	0.176	0.1764	0.1746	0.18	0.2094	0.22	RANDOM	23.293

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]
1.258			-1.408		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.682
r_dihedral_angle_4_deg	16.861
r_dihedral_angle_3_deg	12.995
r_dihedral_angle_other_3_deg	9.873
r_dihedral_angle_1_deg	6.132
r_lrange_it	5.682
r_lrange_other	5.681
r_scangle_it	4.37
r_scangle_other	4.368
r_scbond_it	2.891
r_scbond_other	2.89
r_mcangle_other	2.786
r_mcangle_it	2.778
r_mcbond_it	1.964
r_mcbond_other	1.941
r_angle_refined_deg	1.656
r_angle_other_deg	1.386
r_symmetry_nbd_refined	0.203
r_nbd_refined	0.197
r_symmetry_nbd_other	0.185
r_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.167
r_nbd_other	0.144
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1652
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing