9TDI | pdb_00009tdi

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
2.52	51.22

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		2024-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.8551	ESRF	ID30B

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	1.06	48.283	99.5	1	17.5	12.1		112352

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	1.06	1.1	95.3		0.527		5.8

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	1.06	48.283	111986	5596	99.256	0.144	0.1431	0.1512	0.1526	0.1588	14.27

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]
0.39			0.39		-0.781

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.9
r_dihedral_angle_4_deg	15.052
r_dihedral_angle_3_deg	9.344
r_lrange_other	7.05
r_lrange_it	7.048
r_dihedral_angle_1_deg	7.039
r_scangle_it	3.772
r_scangle_other	3.771
r_scbond_it	2.721
r_scbond_other	2.721

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.9
r_dihedral_angle_4_deg	15.052
r_dihedral_angle_3_deg	9.344
r_lrange_other	7.05
r_lrange_it	7.048
r_dihedral_angle_1_deg	7.039
r_scangle_it	3.772
r_scangle_other	3.771
r_scbond_it	2.721
r_scbond_other	2.721
r_angle_refined_deg	1.945
r_mcbond_it	1.656
r_angle_other_deg	1.523
r_mcangle_other	1.509
r_mcangle_it	1.508
r_mcbond_other	1.047
r_symmetry_nbd_refined	0.304
r_nbd_other	0.26
r_nbd_refined	0.233
r_symmetry_xyhbond_nbd_refined	0.231
r_xyhbond_nbd_refined	0.205
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.177
r_metal_ion_refined	0.143
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.019
r_gen_planes_refined	0.012
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	423
Heterogen Atoms	144

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.