9BE0

GC-centric NF-kappaB RelA binding DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PEG3350 8%, Sodium Acetate pH 3.5 100 mM, Zinc Acetate 50 mM

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.857	α = 90.14
b = 46.85	β = 90.2
c = 99.289	γ = 60.02

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	PIXEL	DECTRIS EIGER X 16M		2021-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	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	2.5	50	90.8	0.062	17	3.8		23456

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	2.5	2.57	73.8		0.4	2.2	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.5	30	22010	1059	91	0.28876	0.28834	0.29748	RANDOM	31.256

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]
0.1	-0.01	-0.15	0.07	0.09	-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	3.315
r_long_range_B_other	3.315
r_angle_other_deg	2.38
r_scangle_other	1.763
r_scbond_it	1.748
r_scbond_other	1.747
r_angle_refined_deg	0.947
r_mcbond_it	0.868
r_chiral_restr	0.051
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.007
r_bond_other_d
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	5451
Solvent Atoms	471
Heterogen Atoms	126

Software

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