6Z9C | pdb_00006z9c

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VBV	1VBV, 5HDW
experimental model	PDB	5HDW	1VBV, 5HDW

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.22	0.2881	0.29	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 R01GM157729.