8CE2 | pdb_00008ce2

X-ray structure of the adduct formed upon reaction of a B-DNA double helical dodecamer with dirhodium tetraacetate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3U2N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	7% (v/v) 2-methyl-2,4-pentanediol, 20 mM MgCl2, 80 mM spermine tetrahydrochloride, and 60 mM sodium cacodylate at pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 25.53	α = 90
b = 40.31	β = 90
c = 65.71	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 PILATUS 6M		2022-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.24	34.36	99.9	0.999	23.2	10.8		19898

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.24	1.26	100		0.785		8.4

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	SAD	FREE R-VALUE	1.24	34.36	19898	972	99.905	0.198	0.1971	0.2	0.2227	0.23	16.356

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]
0.665			0.468		-1.134

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	4.527
r_lrange_other	3.997
r_angle_refined_deg	3.073
r_scangle_it	2.851
r_scangle_other	2.849
r_scbond_it	1.959
r_scbond_other	1.958
r_angle_other_deg	0.495
r_nbtor_refined	0.256
r_symmetry_nbd_other	0.214
r_chiral_restr	0.17
r_symmetry_xyhbond_nbd_refined	0.17
r_xyhbond_nbd_refined	0.166
r_nbd_refined	0.153
r_nbd_other	0.138
r_symmetry_nbtor_other	0.09
r_symmetry_nbd_refined	0.076
r_gen_planes_refined	0.039
r_bond_refined_d	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	486
Solvent Atoms	168
Heterogen Atoms	4

Software

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