3ZYD | pdb_00003zyd

Crystal structure of 3C protease of coxsackievirus B3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VB0	PDB ENTRY 2VB0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5		100 MM TRIS-HCL PH 8.5, 0.2 M MAGNESIUM CHLORIDE, AND 22% PEG 4000; SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.85	α = 90
b = 64.38	β = 116.41
c = 39.36	γ = 90

Symmetry
Space Group	C 1 2 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	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1		BESSY	14.1

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	1.7	24.82	99.8	0.05	12.3	3.8		18920		2

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	1.7	1.79	99.6		0.41	2.8	3.8

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 (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 2VB0	1.7	47.02	17942	977	99.69	0.19358	0.19182	0.19	0.22452	0.23	RANDOM	27.888

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]
0.6		1.15	-1.43		1.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.216
r_dihedral_angle_4_deg	23.481
r_dihedral_angle_3_deg	16.362
r_dihedral_angle_1_deg	6.26
r_scangle_it	4.669
r_scbond_it	2.921
r_mcangle_it	1.897
r_angle_refined_deg	1.675
r_mcbond_it	1.066
r_chiral_restr	0.119
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1406
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing