3ZN5 | pdb_00003zn5

VP16, a capsid protein of bacteriophage P23-77 (VP16-virus-derived)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZMO	PDB CODE 3ZMO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP			SITTING DROP VAPOUR DIFFUSION SYSTEM, MICROLITER DROPS OF PURIFIED P23-77 VIRION (PROTEIN CONCENTRATION 2.4 MG/ML, SAMPLE BUFFER 20 MM TRIS-HCL PH 7.5, 5 MM MGCL2 AND 150 MM NACL) MIXED 1:1 WITH SOLUTION CONSISTING OF 0.1 M CITRIC ACID PH 3.5, 20 MM TRIS-HCL PH 7.5, 5 MM MGCL2, 150 MM NACL AND 25%(W/V) PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.41	α = 90
b = 77.05	β = 90
c = 403	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2012-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24		Diamond	I24

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	2.36	42.16	99.1	0.11	7.5	3.2		54151			52.18

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	2.36	2.42	99.6		1.14	1.3	3.3

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 CODE 3ZMO	2.36	42.16	53974	2743	98.59	0.1946	0.1925	0.2	0.2344	0.24	RANDOM	52.25

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]
-10.2165			-0.8751		11.0916

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	16.27
t_omega_torsion	3.13
t_angle_deg	1.07
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10375
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	4

Software

Software
Software Name	Purpose
BUSTER	refinement
xia2	data reduction
XDS	data reduction
xia2	data scaling
PHASER	phasing