9NPU | pdb_00009npu

Pre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate containing template ribonucleotide opposite primer terminus, and incoming dUMPNPP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7M07

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	294	68 mM Na cacodylate pH 6.5, 20.4% (w/v) PEG8000, 136 mM ammonium sulfate, 12% (v/v) glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.204	α = 90
b = 59.923	β = 90
c = 140.096	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	PIXEL	DECTRIS EIGER X 9M		2025-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.9202	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.63	41.01	100	0.11	0.116	0.035	0.999	11	10.4		60232			19.95

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.63	1.69	100		1.541	1.631	0.526	0.407	1.4	9.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	1.63	40.99	1.35	60225	3029	99.98	0.1792	0.1781	0.1794	0.1992	0.2	random	31.75

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.9685
f_angle_d	1.0826
f_chiral_restr	0.0613
f_bond_d	0.0117
f_plane_restr	0.0109

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2463
Nucleic Acid Atoms	427
Solvent Atoms	265
Heterogen Atoms	48

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
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.