3NCI | pdb_00003nci

RB69 DNA Polymerase Ternary Complex with dCTP Opposite dG at 1.8 angstrom resolution

X-RAY DIFFRACTION

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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	micro-batch vapor-diffusion	6.5	293	8%(w/v) PEG 350 monomethyl ether (MME),160 mM CaCl2, and 100 mM NaCacodylate (pH 6.5), micro-batch vapor-diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.504	α = 90
b = 119.404	β = 90
c = 129.763	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	100	CCD	ADSC QUANTUM 315	mirrors	2009-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9095	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	1.79	50	94.9	0.077	13.7	3.4	104627	99370		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	1.8	1.86	74		0.813	0.86	1.9	8061

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 (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	1.79	50	1	105399	99370	5207	94.28	0.17607	0.17474	0.1805	0.20136	0.2097	RANDOM	26.126

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]
0.16			-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.219
r_dihedral_angle_4_deg	13.287
r_dihedral_angle_3_deg	13.024
r_dihedral_angle_1_deg	4.863
r_scangle_it	2.987
r_scbond_it	1.907
r_mcangle_it	1.66
r_angle_refined_deg	1.005
r_mcbond_it	0.91
r_chiral_restr	0.068
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7374
Nucleic Acid Atoms	630
Solvent Atoms	1373
Heterogen Atoms	31

Software

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