8FIJ

Wild type APOBEC3A in complex with TT(FdZ)-hairpin inhibitor (crystal form 2)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5KEG	Stripped of water, Zn2+, Cl- and ssDNA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		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 hexaphosphate (phytic acid) and 45 % pentaerythritol propoxylate (5/4 PO/OH)

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.943	α = 90
b = 56.365	β = 104.985
c = 90.113	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	2021-09-23	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	2.799	48.291	97.8	0.183	0.118	0.979	4.5	3.3		11861			57

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	2.8	2.95	92.8		1.157	0.735	0.466	0.8	3.4

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	2.799	48.291	11852	623	97.724	0.261	0.2577	0.3182	RANDOM	60.975

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]
4.278		1.154	-2.679		-1.939

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.612
r_dihedral_angle_4_deg	23.042
r_dihedral_angle_3_deg	15.86
r_lrange_it	10.495
r_lrange_other	10.44
r_dihedral_angle_1_deg	7.144
r_scangle_it	5.221
r_scangle_other	5.169
r_mcangle_it	5.097
r_mcangle_other	5.096
r_scbond_it	3.131
r_mcbond_it	3.098
r_mcbond_other	3.085
r_scbond_other	3.056
r_angle_refined_deg	1.64
r_angle_other_deg	1.352
r_nbd_other	0.288
r_symmetry_nbd_other	0.236
r_nbd_refined	0.226
r_symmetry_xyhbond_nbd_other	0.215
r_symmetry_nbd_refined	0.215
r_xyhbond_nbd_refined	0.213
r_nbtor_refined	0.192
r_symmetry_xyhbond_nbd_refined	0.101
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.087
r_metal_ion_refined	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.006
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2924
Nucleic Acid Atoms	404
Solvent Atoms	2
Heterogen Atoms	32

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