9TD0 | pdb_00009td0

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
2.53	51.36

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	2.07	48.34	100	0.994	6.73	10.8		15289

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	2.07	2.12	100		0.571

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	2.07	48.337	15289	775	99.987	0.178	0.1755	0.1862	0.2214	0.2295	29.863

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]
1.45			1.45		-2.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.477
r_dihedral_angle_4_deg	21.202
r_dihedral_angle_3_deg	12.104
r_dihedral_angle_1_deg	7.149
r_lrange_it	4.953
r_lrange_other	4.889
r_scangle_it	3.708
r_scangle_other	3.686
r_mcangle_it	2.692
r_mcangle_other	2.691

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.477
r_dihedral_angle_4_deg	21.202
r_dihedral_angle_3_deg	12.104
r_dihedral_angle_1_deg	7.149
r_lrange_it	4.953
r_lrange_other	4.889
r_scangle_it	3.708
r_scangle_other	3.686
r_mcangle_it	2.692
r_mcangle_other	2.691
r_scbond_it	2.677
r_scbond_other	2.657
r_mcbond_it	2.041
r_mcbond_other	2.028
r_angle_refined_deg	1.736
r_angle_other_deg	1.314
r_symmetry_xyhbond_nbd_refined	0.311
r_xyhbond_nbd_other	0.213
r_nbd_other	0.204
r_nbd_refined	0.191
r_symmetry_nbd_refined	0.189
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.159
r_symmetry_xyhbond_nbd_other	0.095
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.076
r_bond_refined_d	0.01
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	152
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.