9TDD | pdb_00009tdd

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	51.38

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	1.749	48.316	99.7	0.984	9.4	8.1		25244

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	1.749	1.78	95.9		0.351		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	1.749	48.316	25143	1274	99.238	0.134	0.1323	0.1331	0.1552	0.1555	10.242

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]
0.734			0.734		-1.468

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.365
r_dihedral_angle_4_deg	14.638
r_dihedral_angle_3_deg	9.929
r_dihedral_angle_1_deg	6.762
r_lrange_it	5.266
r_lrange_other	5.258
r_scangle_it	3.283
r_scangle_other	3.283
r_scbond_it	2.356
r_scbond_other	2.355

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.365
r_dihedral_angle_4_deg	14.638
r_dihedral_angle_3_deg	9.929
r_dihedral_angle_1_deg	6.762
r_lrange_it	5.266
r_lrange_other	5.258
r_scangle_it	3.283
r_scangle_other	3.283
r_scbond_it	2.356
r_scbond_other	2.355
r_angle_refined_deg	1.973
r_mcangle_other	1.441
r_angle_other_deg	1.435
r_mcangle_it	1.434
r_mcbond_it	1.019
r_mcbond_other	0.9
r_symmetry_nbd_refined	0.346
r_nbd_other	0.286
r_nbd_refined	0.22
r_symmetry_nbd_other	0.191
r_symmetry_xyhbond_nbd_refined	0.185
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.163
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.085
r_metal_ion_refined	0.067
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	242
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.