9T8F | pdb_00009t8f

Crystal structure of trabectedin bound to 10-mer duplex DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		ideal B-DNA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.35	295	MPD, potassium chloride, lithium chloride, spermine

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.078	α = 90
b = 40.942	β = 90
c = 234.506	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		2024-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9793	ALBA	XALOC

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	2.4	25.9	99.19	0.072	0.085	0.043	0.998	7	3.8		10587

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	2.4	2.6	99.53		1.15	1.345	0.691	0.662		3.7

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	2.4	25.9	9980	553	99.528	0.229	0.2263	0.2301	0.2856	0.2873	72.766

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]
6.303			1.184		-7.487

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.133
r_lrange_it	14.249
r_lrange_other	14.247
r_scangle_it	10.095
r_scangle_other	10.093
r_scbond_it	6.733
r_scbond_other	6.733
r_dihedral_angle_other_2_deg	3.828
r_angle_refined_deg	1.972
r_angle_other_deg	0.49
r_symmetry_xyhbond_nbd_refined	0.284
r_nbd_other	0.265
r_nbtor_refined	0.263
r_symmetry_nbd_other	0.25
r_nbd_refined	0.244
r_xyhbond_nbd_refined	0.186
r_symmetry_nbd_refined	0.163
r_metal_ion_refined	0.16
r_symmetry_nbtor_other	0.092
r_symmetry_xyhbond_nbd_other	0.09
r_chiral_restr	0.073
r_gen_planes_refined	0.012
r_bond_refined_d	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1616
Solvent Atoms	8
Heterogen Atoms	269

Software

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