7SKM | pdb_00007skm

Complex between S. aureus aureolysin and wt IMPI.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BQB	1BQB, 3SSB
experimental model	PDB	3SSB	1BQB, 3SSB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	Best crystals of aureolysin in complex with either IMPI variant were obtained at 20 degrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase:inhibitor molar ratio of 1:2.5) in 50 mM Tris-HCl, 150 mM sodium chloride, 1.6 mM calcium chloride, 8.3 microM zinc chloride, pH 8.0, which was mixed with reservoir solution comprising 0.1 M Bis-Tris, 25% (w/v) PEG 3350, pH 5.5.

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.14	α = 90
b = 68.14	β = 90
c = 166.18	γ = 90

Symmetry
Space Group	P 41

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 6M		2020-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9793	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.85	52.7	100	0.149	0.042	0.999	14.7	13.6		64323			42.2

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	1.85	1.96			2.772	0.788	0.63	1.9

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1BQB, 3SSB	1.85	52.689	64322	724	99.966	0.165	0.1644	0.17	0.2186	0.21	38.072

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]
11.211			11.211		-22.422

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.58
r_dihedral_angle_3_deg	16.598
r_dihedral_angle_4_deg	12.465
r_dihedral_angle_1_deg	7.262
r_lrange_it	5.055
r_scangle_it	2.802
r_mcangle_it	2.54
r_scbond_it	1.974
r_mcbond_it	1.787
r_angle_refined_deg	1.644
r_nbtor_refined	0.276
r_symmetry_nbd_refined	0.181
r_nbd_refined	0.159
r_chiral_restr	0.143
r_xyhbond_nbd_refined	0.097
r_symmetry_xyhbond_nbd_refined	0.094
r_gen_planes_refined	0.009
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5708
Nucleic Acid Atoms
Solvent Atoms	709
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing