2RDI

Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JX4	PDB ENTRY 1JX4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.9	294	20% PEG3350, 0.2M lithium nitrate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.927	α = 90
b = 51.069	β = 98.08
c = 86.026	γ = 90

Symmetry
Space Group	C 1 2 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	IMAGE PLATE	MAR scanner 345 mm plate		2005-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.92	30	93.8	0.043	16.8	3	30796	28887		-1	37.479

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.92	1.95	90.6		0.507		2.5	1393

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	PDB ENTRY 1JX4	1.92	20.35	-1	29312	27934	1217	100	0.207	0.207	0.205	0.247	RANDOM	46.44

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]
0.01					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.645
r_dihedral_angle_4_deg	19.366
r_dihedral_angle_3_deg	17.554
r_dihedral_angle_1_deg	6.629
r_scangle_it	2.815
r_scbond_it	1.849
r_angle_refined_deg	1.427
r_mcangle_it	1.116
r_mcbond_it	0.738
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.645
r_dihedral_angle_4_deg	19.366
r_dihedral_angle_3_deg	17.554
r_dihedral_angle_1_deg	6.629
r_scangle_it	2.815
r_scbond_it	1.849
r_angle_refined_deg	1.427
r_mcangle_it	1.116
r_mcbond_it	0.738
r_nbtor_refined	0.303
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.207
r_xyhbond_nbd_refined	0.175
r_symmetry_hbond_refined	0.169
r_chiral_restr	0.104
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2701
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	13

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
PHASER	phasing

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.