6Z9C

Structure of human POLDIP2, a multifaceted adaptor protein in metabolism and genome stability

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Calcium acetate hydrate 0.1M Sodium cacodylate pH 6.5 40% (v/v) PEG 300

Crystal Properties
Matthews coefficient	Solvent content
2.79	56.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.138	α = 90
b = 120.138	β = 90
c = 49.516	γ = 120

Symmetry
Space Group	P 62

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	Bruker PHOTON II	Microfocus Source	2019-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER IMUS MICROFOCUS	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.687	104.042	99.6	0.147	0.159	0.058	13.2	7.1		11561			45.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.69	2.83	98.7		2.049	2.049	2.397	1.216	0.4	3.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1VBV, 5HDW	2.8	23.88	9711	524	99.67	0.2199	0.2163	0.2881	RANDOM	42.602

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]
-0.2	-0.1		-0.2		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.173
r_dihedral_angle_3_deg	22.487
r_dihedral_angle_4_deg	22.133
r_dihedral_angle_1_deg	9.06
r_angle_refined_deg	1.608
r_angle_other_deg	1.178
r_chiral_restr	0.062
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.173
r_dihedral_angle_3_deg	22.487
r_dihedral_angle_4_deg	22.133
r_dihedral_angle_1_deg	9.06
r_angle_refined_deg	1.608
r_angle_other_deg	1.178
r_chiral_restr	0.062
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2130
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	1

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM2	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.