24QI | pdb_000024qi

Crystal structure of a tailspike depolymerase (Belisarius_gp86) from Acinetobacter phage Belisarius

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		288	Bis-tris pH 5.5, 2.4M NaCl

Crystal Properties
Matthews coefficient	Solvent content
5.87	79.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.975	α = 90
b = 100.975	β = 90
c = 784.525	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 2M		2024-02-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS SIRIUS BEAMLINE MANACA	0.977180	LNLS SIRIUS	MANACA

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	2.2	49.67	99.9	0.305	0.317	0.084	0.957	8.2	14.4		79321

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	2.2	2.24		100	1.936	2.007	0.523	0.75		14.5

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	2.2	49.67	75166	3993	99.64	0.21119	0.2104	0.216	0.2261	0.2293	RANDOM	49.898

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]
-0.37	-0.18		-0.37		1.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.137
r_dihedral_angle_4_deg	17.38
r_dihedral_angle_3_deg	14.481
r_dihedral_angle_1_deg	9.72
r_long_range_B_other	9.552
r_long_range_B_refined	9.551
r_mcangle_it	8.797
r_mcangle_other	8.797
r_scangle_other	8.777
r_scbond_it	6.426
r_scbond_other	6.425
r_mcbond_it	6.338
r_mcbond_other	6.337
r_angle_refined_deg	1.924
r_angle_other_deg	1.361
r_chiral_restr	0.091
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.003
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4379
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	32

Software

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