3NAE | pdb_00003nae

RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Guanidinohydantoin

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	15%(w/v) PEG 350 monomethyl ether (MME), 150 mM CaCl2, and 100 mM NaCacodylate (pH 6.5), micro-batch vapor-diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.013	α = 90
b = 119.783	β = 90
c = 130.727	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		2010-03-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.10000	NSLS	X25

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	50	93.7	0.078	14.3	4.5	74483	69794		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)
	2	2.07	75.8		1	0.958	3.2	5982

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	2.003	35.24	1	75863	69794	3673	92	0.19596	0.19407	0.1947	0.23092	0.2332	RANDOM	27.263

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]
-0.73			0.9		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.029
r_dihedral_angle_3_deg	14.201
r_dihedral_angle_4_deg	13.422
r_dihedral_angle_1_deg	4.889
r_scangle_it	3.701
r_scbond_it	2.422
r_mcangle_it	2.182
r_mcbond_it	1.231
r_angle_refined_deg	1.106
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7367
Nucleic Acid Atoms	630
Solvent Atoms	704
Heterogen Atoms	34

Software

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