3ZMN | pdb_00003zmn

VP17, a capsid protein of bacteriophage P23-77

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7		SITTING DROP VAPOUR DIFFUSION SYSTEM, MICROLITER DROPS OF PROTEIN(2-3 MG/ML IN 20 MM TRIS-BUFFER PH 7.4) MIXED 1:1 WITH SOLUTION CONSISTING OF 1.9 M SODIUM FORMATE AND 0.1 M BIS-TRIS BUFFER PH 7.

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.21	α = 90
b = 107.21	β = 90
c = 233.78	γ = 120

Symmetry
Space Group	P 61 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	ADSC CCD		2010-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

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	2.26	59.7	100	0.08	38.6	35.5		37893			49.88

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	2.26	2.32	100		0.92	5.3	36.6

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	SIRAS	THROUGHOUT	NONE	2.26	43.94	37808	1890	99.38	0.1868	0.1855	0.19	0.2132	0.22	RANDOM	51.44

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]
1.6185			1.6185		-3.2371

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	17.5
t_omega_torsion	3.55
t_angle_deg	1.14
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	3607
Nucleic Acid Atoms
Solvent Atoms	424
Heterogen Atoms

Software

Software
Software Name	Purpose
ARP/wARP	model building
xia2	data scaling
xia2	phasing
SHELXD	phasing
autoSHARP	phasing
ARP/wARP	phasing
BUSTER	refinement