7VUP

Structure of NF-kB p52 homodimer bound to +1/-1 swap P-Selectin kB DNA fragment

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A3Q

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	51.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.987	α = 90
b = 84.289	β = 90
c = 140.565	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	3.4	46.85	99.7	0.998	9.6	13		14272

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	3.4	3.58			0.782

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	3.4	45.451	14233	690	99.699	0.272	0.2712	0.2858	156.456

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]
15.984			2.19		-18.174

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.02
r_lrange_it	25.429
r_lrange_other	25.428
r_dihedral_angle_3_deg	18.325
r_mcangle_it	17.231
r_mcangle_other	17.229
r_scangle_it	15.361
r_scangle_other	15.359
r_dihedral_angle_4_deg	14.484
r_mcbond_other	10.764
r_mcbond_it	10.762
r_scbond_it	9.381
r_scbond_other	9.381
r_dihedral_angle_1_deg	7.722
r_angle_refined_deg	1.735
r_angle_other_deg	1.328
r_symmetry_xyhbond_nbd_refined	0.706
r_xyhbond_nbd_other	0.509
r_symmetry_nbd_refined	0.324
r_nbd_other	0.305
r_symmetry_nbd_other	0.21
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.184
r_ncsr_local_group_1	0.119
r_chiral_restr	0.115
r_ext_dist_refined_d	0.094
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4668
Nucleic Acid Atoms	691
Solvent Atoms
Heterogen Atoms

Software

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