3SJJ | pdb_00003sjj

RB69 DNA Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the presence of Mn2+

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IG9	PDB ENTRY 1IG9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH VAPOR DIFFUSION	6.5	293.15	150 mM calcium chloride, 1% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, MICROBATCH VAPOR DIFFUSION, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.56	α = 90
b = 118.217	β = 90
c = 130.108	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	77	CCD	ADSC QUANTUM 315	mirrors	2007-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9795	APS	24-ID-E

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	2.35	50	89.4	0.123	10	4.1	51283	45847	2	1

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	2.35	2.43	77.9		0.778	1	2.3	3930

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB ENTRY 1IG9	2.38	47.25	2	2	46537	42465	2286	91.25	0.20482	0.20164	0.2	0.26543	0.26	RANDOM	53.893

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]
-1.01			0.63		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.54
r_dihedral_angle_3_deg	16.308
r_dihedral_angle_4_deg	16.066
r_dihedral_angle_1_deg	5.482
r_scangle_it	4.909
r_scbond_it	3.327
r_mcangle_it	3.012
r_mcbond_it	1.732
r_angle_refined_deg	1.121
r_chiral_restr	0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.54
r_dihedral_angle_3_deg	16.308
r_dihedral_angle_4_deg	16.066
r_dihedral_angle_1_deg	5.482
r_scangle_it	4.909
r_scbond_it	3.327
r_mcangle_it	3.012
r_mcbond_it	1.732
r_angle_refined_deg	1.121
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7343
Nucleic Acid Atoms	630
Solvent Atoms	138
Heterogen Atoms	35

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.