7CLI

Structure of NF-kB p52 homodimer bound to P-Selectin kB DNA fragment

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.1M Sodium malonate, pH 4.0, 0.2M CsCl, 5% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.495	α = 90
b = 85.37	β = 90
c = 140.29	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	PIXEL	DECTRIS PILATUS3 6M		2019-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97852	SSRF	BL19U1

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	45.63	95.4	0.999	14.3	14		19950

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	3.16	98.2		0.767	1.9	14.2

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	42.722	19898	973	94.906	0.238	0.236	0.2753	107.301

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]
-0.378			9.796		-9.418

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.349
r_lrange_it	19.595
r_lrange_other	19.595
r_dihedral_angle_3_deg	18.677
r_dihedral_angle_4_deg	16.767
r_mcangle_it	13.045
r_mcangle_other	13.044
r_scangle_it	12.281
r_scangle_other	12.28
r_mcbond_it	8.32
r_mcbond_other	8.317
r_scbond_it	7.629
r_scbond_other	7.628
r_dihedral_angle_1_deg	7.268
r_angle_refined_deg	1.78
r_angle_other_deg	1.433
r_symmetry_nbd_refined	0.268
r_nbd_other	0.233
r_symmetry_nbd_other	0.222
r_nbd_refined	0.219
r_ncsr_local_group_1	0.209
r_xyhbond_nbd_refined	0.208
r_nbtor_refined	0.186
r_symmetry_xyhbond_nbd_other	0.148
r_ext_dist_refined_d	0.14
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.087
r_symmetry_xyhbond_nbd_refined	0.074
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4634
Nucleic Acid Atoms	713
Solvent Atoms	12
Heterogen Atoms

Software

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