9E92 | pdb_00009e92

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/substrate/cofactor mix: 28 mg/ml R699, 10 mM UDP glucose, 10 mM MnCl2, 0.15 g/ml glucose, 0.15 g/ml galactose. Mother liquor: 0.1 M HEPES pH 7, 10% (w/v) PEG 6000. The ratio of mix and mother liquor was at 1:1.

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.153	α = 90
b = 124.998	β = 118.295
c = 72.757	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		2023-02-28	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	1.5	62.5	98.4	0.059	0.998	13.3	6.8		171464

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	1.5	1.52			0.602	0.857	1.8	6.3

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	1.5	60.965	171272	8633	98.733	0.167	0.1657	0.1674	0.189	0.1911	20.922

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]
0.197		-0.376	1.682		-0.933

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.906
r_dihedral_angle_3_deg	12.091
r_dihedral_angle_1_deg	6.762
r_lrange_it	5.881
r_dihedral_angle_2_deg	5.853
r_lrange_other	5.806
r_scangle_it	4.697
r_scangle_other	4.696
r_scbond_it	3.103
r_scbond_other	3.102
r_mcangle_it	2.665
r_mcangle_other	2.665
r_mcbond_it	1.844
r_mcbond_other	1.842
r_angle_refined_deg	1.8
r_angle_other_deg	0.624
r_nbd_refined	0.223
r_nbtor_refined	0.181
r_symmetry_nbd_other	0.176
r_symmetry_nbd_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.168
r_nbd_other	0.146
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.098
r_ncsr_local_group_1	0.091
r_symmetry_nbtor_other	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7306
Nucleic Acid Atoms
Solvent Atoms	883
Heterogen Atoms	147

Software

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