Experiment: 6C1Y

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3C2I	Protein coordinates from PDB entry 3c2i. DNA coordinates from a currently unpublished model.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	291	25% PEG3350, 0.1 M ammonium sulfate, 0.1 M tris

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.753	α = 68.15
b = 47.359	β = 89.83
c = 54.623	γ = 65.98

Symmetry
Space Group	P 1

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	MARMOSAIC 300 mm CCD		2013-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97945	APS	23-ID-B

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	2.3	39.85	96.3	0.068	0.091	0.06	0.992	10.1	2.2		14585

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	2.3	2.38	84.2		0.449	0.601	0.397	0.718		2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Protein coordinates from PDB entry 3c2i. DNA coordinates from a currently unpublished model.	2.3	39.85	13799	785	96.3	0.2334	0.2306	0.2857	65.544

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]
-4.22	-1.93	1.86	1.74	-2.26	-2.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.819
r_dihedral_angle_4_deg	28.612
r_dihedral_angle_3_deg	15.157
r_dihedral_angle_1_deg	5.819
r_mcangle_it	3.472
r_mcbond_other	2.296
r_mcbond_it	2.294
r_angle_refined_deg	1.669
r_angle_other_deg	1.316
r_chiral_restr	0.089

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.819
r_dihedral_angle_4_deg	28.612
r_dihedral_angle_3_deg	15.157
r_dihedral_angle_1_deg	5.819
r_mcangle_it	3.472
r_mcbond_other	2.296
r_mcbond_it	2.294
r_angle_refined_deg	1.669
r_angle_other_deg	1.316
r_chiral_restr	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1090
Nucleic Acid Atoms	976
Solvent Atoms
Heterogen Atoms	3

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
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.