9TDC | pdb_00009tdc

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	51.43

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 9M		2024-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8731	ESRF	ID23-2

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	1.553	48.339	87.9	0.997	16.2	10.7		32424

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	1.553	1.57			0.731	1.5	4.2

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	1.553	48.339	32170	1617	89.091	0.126	0.1243	0.1255	0.1533	0.1544	19.187

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]
0.926			0.926		-1.853

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.861
r_dihedral_angle_4_deg	14.587
r_dihedral_angle_3_deg	10.356
r_dihedral_angle_1_deg	6.777
r_lrange_it	6.064
r_lrange_other	6.064
r_scangle_it	4.367
r_scangle_other	4.366
r_scbond_it	3.45
r_scbond_other	3.449

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.861
r_dihedral_angle_4_deg	14.587
r_dihedral_angle_3_deg	10.356
r_dihedral_angle_1_deg	6.777
r_lrange_it	6.064
r_lrange_other	6.064
r_scangle_it	4.367
r_scangle_other	4.366
r_scbond_it	3.45
r_scbond_other	3.449
r_angle_refined_deg	2.234
r_mcangle_other	1.877
r_mcangle_it	1.87
r_mcbond_it	1.648
r_angle_other_deg	1.506
r_mcbond_other	1.368
r_nbd_refined	0.218
r_symmetry_nbd_other	0.197
r_nbd_other	0.193
r_symmetry_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.121
r_symmetry_nbd_refined	0.116
r_symmetry_nbtor_other	0.089
r_metal_ion_refined	0.072
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
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	268
Heterogen Atoms	174

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.