8CMK | pdb_00008cmk

Transportin-3 TNPO3 in complex with RSY region of CIRBP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4C0P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	0.5ul Protein (TNPO3) 12mg/ml with 0.2ul Ligand (CIRBP) 4.4mg/ml and 0.1ul seeding stock were mixed with 0.5ul of condition. Condition: 0.1M Sodium HEPES, 0.1M MOPS (acid), 7.5pH, 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350, 0.05% w/v D-Salicin, 0.05% w/v Esculin hydrate, 0.05% w/v Quinine hemisulfate salt monohydrate, 0.05% w/v Tryptamine, 0.05% w/v Arbutin (in 50% EtOH) Protein and Ligand in 50mM Tris, 150mM NaCl, 2mM TCEP, 0.04% NaN3, pH: 7.5 Buffer

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.526	α = 90
b = 101.805	β = 111.128
c = 114.133	γ = 90

Symmetry
Space Group	P 1 21 1

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 EIGER2 X 16M		2021-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033220	PETRA III, DESY	P11

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	2.94	48.72	98.5	0.094	0.13	0.09	0.996	8	3.5		43555

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	2.94	3.06			0.672	0.923	0.629	0.509		3.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.945	48.715	43523	2105	98.273	0.25	0.2464	0.24	0.3166	0.32	83.416

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]
-0.559		1.168	-1.677		1.027

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.25
r_dihedral_angle_3_deg	15.385
r_lrange_other	14.689
r_lrange_it	14.688
r_mcangle_it	7.991
r_mcangle_other	7.991
r_scangle_it	7.825
r_scangle_other	7.825
r_dihedral_angle_2_deg	7.16
r_dihedral_angle_1_deg	7.051
r_mcbond_it	4.908
r_mcbond_other	4.908
r_scbond_it	4.629
r_scbond_other	4.627
r_angle_refined_deg	1.577
r_symmetry_xyhbond_nbd_refined	0.605
r_angle_other_deg	0.506
r_symmetry_nbd_refined	0.496
r_nbd_other	0.469
r_nbd_refined	0.208
r_symmetry_nbd_other	0.169
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.074
r_symmetry_nbtor_other	0.073
r_symmetry_xyhbond_nbd_other	0.058
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14632
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing