9T9D | pdb_00009t9d

Crystal structure of PM54 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	7	295	25% polyethylene glycol 400, 50 mM MES pH 6.5, 50 mM KCl, 100 mM LiCl and 12 mM spermine

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.43	α = 90
b = 126.688	β = 90
c = 43.387	γ = 90

Symmetry
Space Group	C 2 2 2

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		2024-07-04	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	2.1	46.258	100	0.042	0.05	0.027	0.999	16.3	6.2		15329			50.9

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	2.1	2.2	99.9		0.988	1.262	0.774	0.588	1.1	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	MOLECULAR REPLACEMENT	FREE R-VALUE	2.1	46.258	15328	748	99.909	0.245	0.2427	0.2442	0.2802	0.2818	59.041

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]
-2.323			5.06		-2.736

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	50.997
r_lrange_other	10.416
r_lrange_it	10.412
r_scangle_it	8.579
r_scangle_other	8.577
r_scbond_it	6.183
r_scbond_other	6.183
r_dihedral_angle_other_2_deg	4.507
r_angle_refined_deg	2.434
r_angle_other_deg	0.596
r_nbd_refined	0.287
r_nbtor_refined	0.266
r_nbd_other	0.225
r_symmetry_nbd_other	0.223
r_xyhbond_nbd_refined	0.214
r_symmetry_nbd_refined	0.204
r_symmetry_nbtor_other	0.098
r_chiral_restr	0.089
r_gen_planes_refined	0.013
r_bond_refined_d	0.007
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	808
Solvent Atoms	32
Heterogen Atoms	332

Software

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