28LX | pdb_000028lx

crystal structure of Dpo31, of a tail-spike protein with depolymerase activity identified in a marine podovirus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	Hanging drops, 2 microL of protein (12 mg/ml) with 1 microL of reservoir solution 1.2 M Ammonium sulfate and 100 mM Citric acid at pH 5.0

Crystal Properties
Matthews coefficient	Solvent content
3.53	65.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.2	α = 90
b = 88.2	β = 90
c = 643.33	γ = 120

Symmetry
Space Group	H 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	ADSC QUANTUM 4		2019-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97911	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.2	49.2	43.7	0.115	0.026	1	18.4	21.2		22469			46.19

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.26	5.7		0.875	0.295	0.787		8.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.2	49.2	22468	1092	43.2	0.253	0.252	0.2412	0.273	0.2582	RANDOM	57.35

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]
-0.3265			-0.3265		0.6531

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	15.99
t_omega_torsion	2.7
t_angle_deg	0.83
t_bond_d	0.005
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	4789
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	40

Software

Software
Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PHASER	phasing
PDB_EXTRACT	data extraction