8OQ0 | pdb_00008oq0

Crystal structure of tailspike depolymerase (APK09_gp48) from Acinetobacter phage APK09

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	288	2% PEG200, 100mM HEPES pH 7.5, 20% tacsimate pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.688	α = 90
b = 88.688	β = 90
c = 421.04	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	PIXEL	DECTRIS PILATUS 6M		2021-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.7749	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.59	72.15	99.1	0.339	0.349	0.081	0.993	10.9	18.5		20409

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.59	2.7		94	2.467	2.566	0.674	0.303		13.6

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.59	72.15	19304	1052	99.26	0.19312	0.18867	0.19	0.27157	0.27	RANDOM	58.755

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]
0.68	0.34		0.68		-2.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.93
r_dihedral_angle_3_deg	20.901
r_dihedral_angle_4_deg	19.604
r_long_range_B_refined	13
r_dihedral_angle_1_deg	10.17
r_mcangle_it	9.961
r_scbond_it	9.171
r_mcbond_it	7.508
r_angle_refined_deg	2.379
r_chiral_restr	0.173
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
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_it
r_scangle_other
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	4588
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction