9TDE | pdb_00009tde

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	25 mM sodium acetate pH 5.5, 20 mM sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.6

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	298	PIXEL	DECTRIS EIGER X 9M		2024-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE MicroMAX	0.9544	MAX IV	MicroMAX

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	1.75	49.48	95.8	0.972	3.76	3.52		25358

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	1.75	1.82	97		0.405		3.53

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	1.75	49.48	25357	1273	95.759	0.168	0.1662	0.1777	0.1916	0.1978	17.338

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]
0.237			0.237		-0.475

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.027
r_dihedral_angle_4_deg	14.594
r_dihedral_angle_3_deg	10.54
r_dihedral_angle_1_deg	6.856
r_lrange_it	4.687
r_lrange_other	4.425
r_scangle_it	2.808
r_scangle_other	2.757
r_scbond_it	1.957
r_mcangle_other	1.818

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.027
r_dihedral_angle_4_deg	14.594
r_dihedral_angle_3_deg	10.54
r_dihedral_angle_1_deg	6.856
r_lrange_it	4.687
r_lrange_other	4.425
r_scangle_it	2.808
r_scangle_other	2.757
r_scbond_it	1.957
r_mcangle_other	1.818
r_mcangle_it	1.817
r_scbond_other	1.795
r_angle_refined_deg	1.518
r_angle_other_deg	1.356
r_mcbond_it	1.199
r_mcbond_other	1.191
r_nbd_refined	0.194
r_nbd_other	0.194
r_symmetry_nbd_other	0.188
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.124
r_symmetry_nbd_refined	0.09
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.068
r_metal_ion_refined	0.042
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
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	197
Heterogen Atoms	14

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.