7VUQ

Structure of NF-kB p52 homodimer bound to A/T-centric P-Selectin kB DNA fragment

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M Sodium malonate, pH 4.0, 50mM CsCl, 2.5% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.453	α = 90
b = 84.627	β = 90
c = 139.427	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	93	PIXEL	DECTRIS EIGER X 16M		2019-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979183	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	3.1	46.48	99.8	0.999	16.1	13.1		18756

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.27			0.934

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1a3q	3.1	40.003	18703	983	99.76	0.226	0.2243	0.2487	131.11

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]
1.769			12.045		-13.814

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.031
r_lrange_it	21.025
r_lrange_other	21.025
r_dihedral_angle_3_deg	19.806
r_mcangle_it	14.806
r_mcangle_other	14.803
r_dihedral_angle_4_deg	14.433
r_scangle_it	14.353
r_scangle_other	14.351
r_mcbond_it	9.688
r_mcbond_other	9.666
r_scbond_it	9.184
r_scbond_other	9.183
r_dihedral_angle_1_deg	7.319
r_angle_refined_deg	1.866
r_angle_other_deg	1.37
r_symmetry_xyhbond_nbd_refined	0.314
r_nbd_other	0.23
r_symmetry_nbd_refined	0.226
r_symmetry_nbd_other	0.222
r_nbd_refined	0.219
r_ncsr_local_group_2	0.213
r_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.187
r_ncsr_local_group_1	0.16
r_chiral_restr	0.124
r_ext_dist_refined_d	0.091
r_symmetry_nbtor_other	0.087
r_symmetry_xyhbond_nbd_other	0.063
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4668
Nucleic Acid Atoms	713
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing