2O8L | pdb_00002o8l

Structure of V8 protease from staphylococcus aureus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QY6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.6	293	PEG 5000 MME, KCl, HEPES, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.43	α = 90
b = 59.43	β = 90
c = 214.01	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	MARMOSAIC 225 mm CCD		2006-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.3317	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.5	19.4	89.8	0.13	0.14	9.95	5.94	65067	58412		5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.5	1.63	92.3		0.418	0.471	3.2	4	11330

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	THROUGHOUT	1QY6	1.5	19.37	32179	32179	1694	100	0.1899	0.1899	0.18839	0.19	0.21867	0.22	RANDOM	10.418

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]
0.03	0.02		0.03		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.873
r_dihedral_angle_4_deg	26.411
r_dihedral_angle_3_deg	13.92
r_dihedral_angle_1_deg	6.853
r_scangle_it	5.407
r_scbond_it	3.509
r_angle_refined_deg	2.366
r_mcangle_it	2.084
r_mcbond_it	1.251
r_metal_ion_refined	0.838
r_symmetry_metal_ion_refined	0.583
r_symmetry_vdw_refined	0.477
r_nbtor_refined	0.338
r_nbd_refined	0.263
r_chiral_restr	0.187
r_xyhbond_nbd_refined	0.176
r_symmetry_hbond_refined	0.172
r_bond_refined_d	0.028
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1653
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	1

Software

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