3P06 | pdb_00003p06

Crystal structure of Tellina virus 1 VP4 protease in the form of an intra-molecular(cis)acyl-enzyme complex.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5	296	reservoir: 21% PEG8000, 0.55M ammonium sulfate. drop: On a coverslip, 1 microliter of VP4 was mixed with 1 microliter of reservoir reagent(21% PEG8000, 0.55M ammonium sulfate) and 1 microliter of 0.2M urea as additive. To aid in crystal nucleation, this drop was seeded with 1 microliter of selenomethionine- labelled crystal from an older drop, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.14	α = 90
b = 59.14	β = 90
c = 208.142	γ = 120

Symmetry
Space Group	P 64 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	100	CCD	MARMOSAIC 300 mm CCD	DCM WITH CRYO-COOLED 1ST CRYSTAL SAGITTALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR.	2010-05-28	M	SAD

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.1	52	99.8	0.107	14.5	11.4		13466		2

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)
	2.1	2.2	98.5		0.35	0.3	4.3	5.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.1	52	13466	12743	662	99.7	0.185	0.182	0.233	0.2461	RANDOM	28.44

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]
-0.02	-0.01		-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.944
r_dihedral_angle_4_deg	17.371
r_dihedral_angle_3_deg	15.683
r_scangle_it	6.446
r_dihedral_angle_1_deg	6.422
r_scbond_it	3.965
r_mcangle_it	2.126
r_angle_refined_deg	1.979
r_mcbond_it	1.186
r_chiral_restr	0.138
r_bond_refined_d	0.024
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1424
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	32

Software

Software
Software Name	Purpose
Mx	data collection
PHENIX	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing