9NEV | pdb_00009nev

Acanthamoeba Polyphaga Mimivirus L230

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6AX6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Protein/cofactor mix: 15mg/ml L230, 500uM FeCl2 Mother Liquor: 0.04 M potassium dihydrogen phosphate, 16 % w/v PEG 8000, 20 % v/v Glycerol The ratio of mix and mother liquor was at 1:1.

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.61	α = 90
b = 109.61	β = 90
c = 84.954	γ = 90

Symmetry
Space Group	P 43 21 2

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		2021-04-05	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)	R Merge I (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	2.3	49.02	100	0.16	0.999	15.7	25.7		23603

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	100		1.002	0.936	4.2	27.1

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	2.3	49.015	23546	1210	99.877	0.207	0.2047	0.2047	0.2509	0.2511	33.423

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]
-0.116			-0.116		0.232

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.623
r_dihedral_angle_3_deg	12.852
r_lrange_it	7.707
r_dihedral_angle_1_deg	7.354
r_dihedral_angle_2_deg	6.809
r_scangle_it	6.194
r_mcangle_it	4.217
r_scbond_it	4.064
r_mcbond_it	2.748
r_angle_refined_deg	1.484
r_nbtor_refined	0.305
r_nbd_refined	0.187
r_symmetry_xyhbond_nbd_refined	0.148
r_xyhbond_nbd_refined	0.122
r_symmetry_nbd_refined	0.122
r_chiral_restr	0.112
r_ncsr_local_group_1	0.095
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3298
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms

Software

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