8CPG | pdb_00008cpg

Structure of the AT-Hook 1 peptide from the mammalian HMGA protein in complex with DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EIL	Chains A and B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	277.15	Crystallization buffer: 0.025mM NiCl2 10 mM MgCl2 2.5% MPD 25 mM NaCaco, pH 6 Final well concentration MPD about 38% Crystallization drops were setup at 285.15 K, using a well solution consisting of aqueous MPD at 17% (v/v) concentration. After three days, the temperature was lowererd to 281.15 K. After 3 days at 281.15K, the solution in the well solution was changed to 25% MPD in water. After 1 week, the temperature was changed to 277.15K. The well solution was interchanged to a MPD solution at 30%. and after 8 days it was replaced by a 38% (v/v) MPD solution.

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.635	α = 90
b = 43.635	β = 90
c = 97.48	γ = 120

Symmetry
Space Group	P 32

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 PILATUS 6M	KB mirrors, Si surface	2017-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97925	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.4	37.79	99.8	0.067	0.072	0.025	0.998	18.5	8.4		40810	-3

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	1.4	1.424			0.579	0.619	0.326	0.922	3.9

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	1.4	37.79	38850	1975	99.81	0.12597	0.12424	0.1286	0.15812	0.1595	RANDOM	14.952

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]
-0.52	-0.26		-0.52		1.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	17.447
r_dihedral_angle_3_deg	12.344
r_dihedral_angle_1_deg	7.548
r_dihedral_angle_2_deg	3.857
r_long_range_B_refined	2.978
r_long_range_B_other	2.73
r_scangle_other	2.725
r_scbond_it	1.893
r_scbond_other	1.891
r_mcangle_it	1.835
r_mcangle_other	1.826
r_rigid_bond_restr	1.815
r_angle_other_deg	1.605
r_angle_refined_deg	1.58
r_mcbond_it	1.405
r_mcbond_other	1.372
r_chiral_restr	0.069
r_gen_planes_refined	0.029
r_bond_refined_d	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.002
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	167
Nucleic Acid Atoms	1426
Solvent Atoms	361
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
pointless	data scaling
PHASER	phasing