4YPL

Crystal structure of a hexameric LonA protease bound to three ADPs

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YPN	4YPN, 1QZM and 1RR9
experimental model	PDB	1QZM	4YPN, 1QZM and 1RR9
experimental model	PDB	1RR9	4YPN, 1QZM and 1RR9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	8.7	295	0.1 M Tris-HCl pH 8.7, 0.1 M CaCl2, 10-13% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 169.044	α = 90
b = 169.128	β = 90
c = 135.361	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	CCD	RAYONIX MX300HE		2014-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.45	50	99.5	0.168	5.6	52050	45968		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.45	3.47	99.6		2.53	5.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4YPN, 1QZM and 1RR9	3.45	30	45968	2447	93.47	0.23859	0.2372	0.2648	RANDOM	66.574

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]
-1.38			1		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.025
r_dihedral_angle_3_deg	22.447
r_dihedral_angle_4_deg	19.299
r_dihedral_angle_1_deg	7.984
r_long_range_B_refined	7.788
r_long_range_B_other	7.788
r_mcangle_it	4.656
r_mcangle_other	4.656
r_scangle_other	4.025
r_angle_other_deg	3.543
r_mcbond_it	2.737
r_mcbond_other	2.737
r_scbond_it	2.244
r_scbond_other	2.244
r_angle_refined_deg	1.517
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	25091
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	267

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
HKL-2000	data scaling