3KD5

Closed ternary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair and phosphonoformic acid.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KD1	PDB entry 3KD1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	5% PEG 20000, 0.1M sodium acetate pH5, 0.1M magnesium acetate, 0.1M Tris HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.855	α = 90
b = 122.481	β = 90
c = 133.371	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	200	IMAGE PLATE	MAR scanner 300 mm plate	Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geomet ry	2009-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.03315	APS	23-ID-B

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	2.7	40	100	0.113	26.9	23.4	36065	36065			86.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.8	100		3.4	21.1	3545

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	isomorphous replacement	THROUGHOUT	PDB entry 3KD1	2.69	30	32507	32507	3470	99.23	0.21939	0.21939	0.21467	0.26317	Test set extracted from 1IG9	38.787

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]
-5.64			0.5		5.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.671
r_dihedral_angle_3_deg	16.703
r_dihedral_angle_4_deg	14.732
r_dihedral_angle_1_deg	4.732
r_angle_refined_deg	0.958
r_chiral_restr	0.067
r_mcbond_it	0.023
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7379
Nucleic Acid Atoms	648
Solvent Atoms	246
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
Blu-Ice	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	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.