4OO6 | pdb_00004oo6

Crystal structure of human KAP-beta2 bound to the NLS of HCC1 (Hepato Cellular Carcinoma protein 1)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FDD	PDB entry 4FDD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.25	298	"Protein (20 MM HEPES, PH 7.3, 110 MM POTASSIUM ACETATE, 2MM MAGNESIUM ACET ATE, 20% GLYCEROL, 2MM DTT); Reservoir (0.2 M Sodiumchloride, 0.8M Sodiumcitrate, 0.1M BisTris pH 6.25 ); Cryo (2.5 M Sodiummalonate)">, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.5	64.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.584	α = 90
b = 162.152	β = 90
c = 68.501	γ = 90

Symmetry
Space Group	P 21 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	ADSC QUANTUM 315r	MIRRORS	2013-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0750	NSLS	X29A

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	2.7	40	99.9	0.102	13.3	5.3	39520	39520			54.3

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	2.7	2.81	99.7		1.295	1.4	5.3	4389

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 4FDD	2.7	40	39470	1977	99.79	0.1912	0.1886	0.18	0.2384	0.23	RANDOM	67.545

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]
-4.24			3.52		0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.117
r_dihedral_angle_4_deg	19.389
r_dihedral_angle_3_deg	16.998
r_mcangle_it	6.521
r_dihedral_angle_1_deg	6.008
r_mcbond_it	4.262
r_mcbond_other	4.261
r_angle_refined_deg	1.44
r_angle_other_deg	0.825
r_chiral_restr	0.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.117
r_dihedral_angle_4_deg	19.389
r_dihedral_angle_3_deg	16.998
r_mcangle_it	6.521
r_dihedral_angle_1_deg	6.008
r_mcbond_it	4.262
r_mcbond_other	4.261
r_angle_refined_deg	1.44
r_angle_other_deg	0.825
r_chiral_restr	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6735
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
XDS	data reduction
XDS	data scaling
PHASER	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.