9CRZ | pdb_00009crz

Acanthamoeba Polyphaga Mimivirus R655

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		277	R655 IMAC elution fractions were digested with PreScission, and the His6 tag was removed by subtraction IMAC. Subtraction IMAC elution fractions were combined and concentrated for crystal trials. Single crystals were obtained through hanging drop vapor diffusion with the Mosquito liquid handling robot (TTPLabtech), utilizing a 200-nL drop with 1:1 mixture of protein solution and mother liquor at 277K. The protein solution has R655 (30 mg/mL) supplemented with 2 mM manganese(II) chloride and 2 mM UDP glucose. The mother liquor has 0.2 M magnesium formate, 20% (w/v) PEG 3350. To harvest the crystals, the crystals were soaked in a 1:1 mixture of 50% glycerol and mother liquor for 2 minutes and cooled in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.634	α = 90
b = 96.213	β = 90
c = 133.454	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	110	PIXEL	DECTRIS EIGER X 16M		2022-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.1	78.17	99.6	0.946	6.3	5.1		46085

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16	99.5		0.706	1.7	5.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	78.167	46000	2234	99.198	0.212	0.2096	0.2116	0.2518	0.2543	31.652

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]
0.623			-2.289		1.667

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.651
r_dihedral_angle_3_deg	11.739
r_dihedral_angle_1_deg	7.032
r_lrange_it	5.105
r_dihedral_angle_2_deg	5.085
r_scangle_it	3.539
r_mcangle_it	2.388
r_scbond_it	2.281
r_mcbond_it	1.588
r_angle_refined_deg	1.023
r_nbtor_refined	0.311
r_nbd_refined	0.191
r_symmetry_nbd_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.16
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.088
r_ncsr_local_group_1	0.087
r_gen_planes_refined	0.005
r_bond_refined_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5114
Nucleic Acid Atoms
Solvent Atoms	451
Heterogen Atoms	52

Software

Software
Software Name	Purpose
DIALS	data collection
xia2	data reduction
Aimless	data scaling
PHENIX	phasing
PHASER	phasing
Coot	model building
REFMAC	refinement