9TD1 | pdb_00009td1

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7PYL

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	278	20 mM sodium acetate pH 5.5, 150 mM sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.46

Symmetry
Space Group	P 41

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 EIGER X 16M		2024-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9763	MAX IV	BioMAX

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	1.94	48.06	100	0.992	3.83	14		18227

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	1.94	1.99	99.9		0.626

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	FOURIER SYNTHESIS	FREE R-VALUE	1.94	48.056	18227	929	99.951	0.222	0.2194	0.2282	0.269	0.2705	35.639

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]
2.158			2.158		-4.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.234
r_dihedral_angle_4_deg	17.657
r_dihedral_angle_3_deg	12.229
r_dihedral_angle_1_deg	6.983
r_lrange_it	5.852
r_lrange_other	5.678
r_scangle_it	3.91
r_scangle_other	3.909
r_mcangle_it	3.672
r_mcangle_other	3.672

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.234
r_dihedral_angle_4_deg	17.657
r_dihedral_angle_3_deg	12.229
r_dihedral_angle_1_deg	6.983
r_lrange_it	5.852
r_lrange_other	5.678
r_scangle_it	3.91
r_scangle_other	3.909
r_mcangle_it	3.672
r_mcangle_other	3.672
r_scbond_it	2.969
r_scbond_other	2.856
r_mcbond_it	2.625
r_mcbond_other	2.605
r_angle_refined_deg	1.676
r_angle_other_deg	1.284
r_nbd_other	0.224
r_symmetry_xyhbond_nbd_refined	0.22
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.199
r_symmetry_nbd_other	0.192
r_symmetry_nbd_refined	0.172
r_nbtor_refined	0.164
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1787
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	87

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.