8FIK

APOBEC3A E72A inactive mutant in complex with ATTC-hairpin DNA substrate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	285	A3A-E72A (50 mM MES pH 6.0, 100 mM NaCl, 1 mM TCEP, 0.2 mM EDTA) was mixed with oligonucleotides (10 mM Tris/HCl pH 7.9, 1 mM EDTA) at 0.85 mM and 1.7 mM respectively. Dilution was done with protein buffer. The mixture was added to crystallization liquid 1 to 1 and the mixture was pipetted on siliconized glass disks and sealed on top of a reservoir of crystallization liquid for hanging drop crystallization at 12 degrees Celsius. The crystallization liquid has the following composition: 100 mM Bicine at pH 6.6, 200 mM NaCl, 20 mM putrescine, 1 mM TCEP, 1 mM inositol hex phosphate (phytic acid) and 45 % pentaerythritol propoxylate (5/4 PO/OH)

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.001	α = 90
b = 57.229	β = 106.478
c = 92.752	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	100	PIXEL	DECTRIS EIGER X 16M	1 vertical and 2 horizontal focussing mirrors	2021-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953739	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.91	48.173	98.4	0.09	0.057	0.996	7.5	3.4		42309			26.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.91	1.96	94.2		0.913	0.589	0.471	1	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5KEG	1.912	48.173	42293	2103	98.37	0.202	0.2001	0.2317	RANDOM	34.801

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]
1.559		0.376	-0.657		-0.957

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.709
r_dihedral_angle_4_deg	20.832
r_dihedral_angle_3_deg	14.828
r_lrange_it	7.399
r_lrange_other	7.399
r_dihedral_angle_1_deg	6.715
r_scangle_it	5.504
r_scangle_other	5.498
r_mcangle_it	3.962
r_mcangle_other	3.962
r_scbond_it	3.409
r_scbond_other	3.399
r_mcbond_it	2.538
r_mcbond_other	2.537
r_angle_refined_deg	1.737
r_angle_other_deg	1.385
r_symmetry_nbd_refined	0.231
r_symmetry_nbd_other	0.215
r_nbd_refined	0.214
r_nbd_other	0.211
r_xyhbond_nbd_refined	0.201
r_nbtor_refined	0.191
r_symmetry_xyhbond_nbd_refined	0.176
r_ncsr_local_group_2	0.145
r_chiral_restr	0.107
r_symmetry_xyhbond_nbd_other	0.105
r_ncsr_local_group_1	0.102
r_metal_ion_refined	0.095
r_symmetry_nbtor_other	0.083
r_gen_planes_refined	0.013
r_bond_refined_d	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3031
Nucleic Acid Atoms	614
Solvent Atoms	157
Heterogen Atoms	55

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
JBluIce-EPICS	data collection
Aimless	data scaling
pointless	data scaling
MOLREP	phasing
Coot	model building