3EDI

Crystal structure of tolloid-like protease 1 (TLL-1) protease domain

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	277	25% PEG 3350, 200mM lithium sulphate, 100mM Bis-Tris-HCl, pH 7.5, vapor diffusion, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.281	α = 90
b = 58.923	β = 104.62
c = 47.444	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2007-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9999	SLS	X10SA

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	1.4	58.9	96.3	0.073	0.044	15.9	3.5	43398	41793		-3	20.8

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)
	1.4	1.44	74.1		0.479	0.327	2.9	2.66	2592

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	1DLE	1.4	29.96	41791	2090	96.39	0.155	0.154	0.182	RANDOM	18.521

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]
-0.14		-0.08	0.11		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.716
r_dihedral_angle_4_deg	16.797
r_dihedral_angle_3_deg	12.887
r_sphericity_free	7.68
r_dihedral_angle_1_deg	6.135
r_sphericity_bonded	5.158
r_scangle_it	5.07
r_scbond_it	4.873
r_rigid_bond_restr	4.479
r_mcangle_it	2.747
r_mcbond_it	1.843
r_angle_refined_deg	1.473
r_symmetry_hbond_refined	0.591
r_symmetry_vdw_refined	0.365
r_nbtor_refined	0.312
r_nbd_refined	0.288
r_xyhbond_nbd_refined	0.256
r_chiral_restr	0.103
r_metal_ion_refined	0.034
r_bond_refined_d	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1598
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	24

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction