9CLE | pdb_00009cle

Importin alpha isoform 2 with synthetic zero net-charge nuclear localization signal

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WV6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	296	0.7 M NaCit, 0.1 M HEPES pH 6.6, 60% glycerol, 10 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.431	α = 90
b = 89.818	β = 90
c = 99.66	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 EIGER X 9M		2023-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9537	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.34	50	100	0.08	0.088	0.034	0.997	6.4	6.4		30438

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.34	2.38	100		0.541	0.588	0.227	0.862		6.6

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.34	49.88	28920	1464	99.83	0.15952	0.15725	0.1659	0.20496	0.2051	RANDOM	44.037

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]
0.37			-1.2		0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.543
r_long_range_B_other	11.257
r_long_range_B_refined	11.246
r_dihedral_angle_2_deg	9.531
r_scangle_other	8.883
r_mcangle_other	5.98
r_mcangle_it	5.976
r_scbond_it	5.883
r_scbond_other	5.881
r_dihedral_angle_1_deg	4.648
r_mcbond_it	4.209
r_mcbond_other	4.193
r_angle_refined_deg	1.367
r_angle_other_deg	0.478
r_chiral_restr	0.071
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3356
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing