4IZK | pdb_00004izk

Crystal structure of yellowtail ascites virus VP4 protease active site mutant (K674A) reveals both an acyl-enzyme complex and an empty active site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4IZJ	PDB entry 4IZJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	296	25% PEG 2000, 0.1 M MES, 0.45 M MAGNESIUM CHLORIDE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
4.79	74.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 273.52	α = 90
b = 273.52	β = 90
c = 273.52	γ = 90

Symmetry
Space Group	F 41 3 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 225 mm CCD	DCM WITH CRYO-COOLED. 1ST CRYSTAL SAGITTALLY BENT. 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR.	2010-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9795	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	2.3	55.8	100	0.105	13.8	8.7	39388	39388			36.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.4	100		0.249	6.5	8.1	5637

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 (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	PDB entry 4IZJ	2.3	55.8	39388	39388	1978	100	0.17394	0.17269	0.1719	0.19685	0.1954	RANDOM	35.166

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.973
r_dihedral_angle_3_deg	15.736
r_dihedral_angle_4_deg	15.075
r_dihedral_angle_1_deg	7.018
r_angle_refined_deg	1.428
r_chiral_restr	0.121
r_gen_planes_refined	0.017
r_bond_refined_d	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3026
Nucleic Acid Atoms
Solvent Atoms	320
Heterogen Atoms	6

Software

Software
Software Name	Purpose
MxDC	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling