Experiment: 2QEF

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	355D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291	Final droplets contain 0.6 mM oligonucleotides, 5% MPD, 20 mM sodium cacodylate, 6 mM spermine tetrahydrochloride, 40 mM KCl and 10 mM MgCl2., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 24.858	α = 90
b = 41.057	β = 90
c = 66.615	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	MAR CCD 165 mm		2007-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-ID

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	1.6	34.94	93	0.067		8.5	9574	8368

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)
	1.6	1.68	62.1		0.133		4.1	821

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 (All)	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	355D	1.6	34.94	2	2	9574	8368	497	93.38	0.18365	0.18112	0.18112	0.2	0.23114	0.24	RANDOM	29.313

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]
1.23			-0.44		-0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	4.893
r_scbond_it	3.735
r_angle_refined_deg	1.596
r_angle_other_deg	1.096
r_nbd_refined	0.526
r_nbd_other	0.251
r_nbtor_refined	0.249
r_symmetry_hbond_refined	0.18
r_xyhbond_nbd_refined	0.174
r_symmetry_vdw_other	0.136

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	4.893
r_scbond_it	3.735
r_angle_refined_deg	1.596
r_angle_other_deg	1.096
r_nbd_refined	0.526
r_nbd_other	0.251
r_nbtor_refined	0.249
r_symmetry_hbond_refined	0.18
r_xyhbond_nbd_refined	0.174
r_symmetry_vdw_other	0.136
r_nbtor_other	0.081
r_chiral_restr	0.064
r_gen_planes_refined	0.024
r_symmetry_vdw_refined	0.008
r_bond_refined_d	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	492
Solvent Atoms	96
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
EPMR	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.