9T8E | pdb_00009t8e

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	292	Sodium malonate, potassium chloride, lithium chloride, spermine

Symmetry
Space Group	P 41 3 2

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 PILATUS3 6M		2024-10-27	M	SINGLE WAVELENGTH

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

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	2.3	39.7	99.95	0.142	0.146	0.032	0.999	16.05	21.1		11334

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	2.3	2.5	100		3.306	3.39	0.745	0.464	1.08	20.7

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	2.3	39.7	10731	567	99.9	0.202	0.2009	0.2005	0.2168	0.2169	55.652

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.749
r_lrange_other	10.608
r_lrange_it	10.007
r_scangle_it	9.554
r_scangle_other	9.548
r_scbond_other	8.373
r_scbond_it	8.351
r_angle_refined_deg	3.73
r_dihedral_angle_other_2_deg	1.463
r_angle_other_deg	0.645

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.749
r_lrange_other	10.608
r_lrange_it	10.007
r_scangle_it	9.554
r_scangle_other	9.548
r_scbond_other	8.373
r_scbond_it	8.351
r_angle_refined_deg	3.73
r_dihedral_angle_other_2_deg	1.463
r_angle_other_deg	0.645
r_symmetry_nbd_refined	0.541
r_nbtor_refined	0.275
r_nbd_refined	0.273
r_nbd_other	0.264
r_symmetry_nbd_other	0.241
r_symmetry_xyhbond_nbd_refined	0.232
r_metal_ion_refined	0.212
r_xyhbond_nbd_refined	0.192
r_chiral_restr	0.121
r_symmetry_nbtor_other	0.107
r_gen_planes_refined	0.026
r_bond_refined_d	0.014
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	404
Solvent Atoms	43
Heterogen Atoms	71

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.