4QR9 | pdb_00004qr9

Crystal structure of two HMGB1 Box A domains cooperating to underwind and kink a DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CKT	PDB entry 1CKT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	0.025M Sodium Cacodylate 0.020M Magnesium Chloride 2.5% MPD (equilibrated against 40% MPD), pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.751	α = 90
b = 84.17	β = 90
c = 94.227	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	PSI PILATUS 6M	Mirrors	2013-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97949	ALBA	XALOC

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	42.12	98.9	0.113	16.025	7.1	23702	23441		-3	32

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	2.07	93.5		0.658	1.9	5.1	2162

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 1CKT	2	42.12	22219	1176	98.78	0.19868	0.19675	0.2042	0.23387	0.2349	RANDOM	42.412

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]
2.43			-1.21		-1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.956
r_dihedral_angle_4_deg	18.229
r_dihedral_angle_3_deg	18.187
r_dihedral_angle_1_deg	5.485
r_angle_other_deg	2.924
r_angle_refined_deg	1.622
r_chiral_restr	0.098
r_bond_refined_d	0.016
r_bond_other_d	0.012
r_gen_planes_refined	0.012
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1234
Nucleic Acid Atoms	808
Solvent Atoms	115
Heterogen Atoms	1

Software

Software
Software Name	Purpose
Xaloc	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling