8RI5 | pdb_00008ri5

Crystal structure of transplatin/B-DNA adduct obtained upon 48 h of soaking

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	293	7-14% (v/v) 2-methyl-2,4-pentanediol (MPD), 20 mM MgCl2, 80 mM spermine tetrahydrochloride, and 60 mM sodium cacodylate pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 25.474	α = 90
b = 40.221	β = 90
c = 65.676	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		2023-10-04	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	1.41	25.47	89.9	0.999	30.5	10		12070

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	1.41	1.45	51.9		0.832	2.5	4.8

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	1.415	25.45	12045	601	89.474	0.192	0.1897	0.2	0.2295	0.24	17.203

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]
0.765			0.262		-1.027

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	4.723
r_lrange_other	4.219
r_angle_refined_deg	3.199
r_scangle_it	3.005
r_scangle_other	3.003
r_scbond_it	2.045
r_scbond_other	2.045
r_angle_other_deg	0.484
r_nbtor_refined	0.252
r_symmetry_nbd_other	0.213
r_chiral_restr	0.162
r_nbd_refined	0.151
r_symmetry_xyhbond_nbd_refined	0.147
r_xyhbond_nbd_refined	0.144
r_nbd_other	0.144
r_symmetry_nbtor_other	0.092
r_symmetry_nbd_refined	0.065
r_gen_planes_refined	0.036
r_bond_refined_d	0.011
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	121
Heterogen Atoms	3

Software

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