3U21 | pdb_00003u21

Crystal structure of a Fragment of Nuclear factor related to kappa-B-binding protein (residues 370-495) (NFRKB) from Homo sapiens at 2.18 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.09M HEPES pH 7.5, 10% glycerol, 1.26M tri-sodium citrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.942	α = 90
b = 60.942	β = 90
c = 130.839	γ = 90

Symmetry
Space Group	P 43 21 2

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	MARMOSAIC 325 mm CCD	double crystal monochromator	2011-06-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97936,0.97915	SSRL	BL9-2

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	2.18	35.466	99.8	0.067	20.78			13560		-3	41.259

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	2.18	2.26	99.9		0.796	2.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.18	35.466	13504	662	99.75	0.2324	0.2305	0.2356	0.2695	0.2737	RANDOM	46.2329

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]
-0.21			-0.21		0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.308
r_dihedral_angle_3_deg	15.037
r_dihedral_angle_4_deg	7.053
r_torsion_it	6.824
r_dihedral_angle_1_deg	5.482
r_angle_it	4.176
r_bond_it	2.782
r_angle_others	2.448
r_angle_refined_deg	1.252
r_angle_other_deg	0.866

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.308
r_dihedral_angle_3_deg	15.037
r_dihedral_angle_4_deg	7.053
r_torsion_it	6.824
r_dihedral_angle_1_deg	5.482
r_angle_it	4.176
r_bond_it	2.782
r_angle_others	2.448
r_angle_refined_deg	1.252
r_angle_other_deg	0.866
r_bond_other	0.478
r_chiral_restr	0.07
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1732
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	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.