9DYT | pdb_00009dyt

Acanthamoeba Polyphaga Mimivirus R699

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		other solved exp. R699 model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	Protein/cofactor mix: 30mg/ml R699, 2mM MnCl2. mother liquor: 0.2 M Ammonium formate, 20% (w/v) PEG 3350 The ratio of mix and mother liquor was at 1:1.

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.821	α = 90
b = 121.696	β = 118.589
c = 72.69	γ = 90

Symmetry
Space Group	P 1 21 1

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		2022-12-13	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	1.8	61.383	98.8	0.079	0.998	10.7	6.8		97211

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	1.8	1.83	99.3		0.908	0.864	1.7	6.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	61.383	97161	4915	98.669	0.191	0.1895	0.1932	0.2199	0.2238	33.623

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]
0.213		-0.825	3.899		-2.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.976
r_dihedral_angle_3_deg	12.821
r_lrange_it	6.925
r_dihedral_angle_1_deg	6.752
r_scangle_it	5.565
r_dihedral_angle_2_deg	5.096
r_mcangle_it	3.834
r_scbond_it	3.695
r_mcbond_it	2.724
r_angle_refined_deg	1.536
r_nbtor_refined	0.317
r_symmetry_nbd_refined	0.213
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.143
r_symmetry_xyhbond_nbd_refined	0.129
r_chiral_restr	0.108
r_ncsr_local_group_1	0.094
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7220
Nucleic Acid Atoms
Solvent Atoms	506
Heterogen Atoms	2

Software

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