9TDF | pdb_00009tdf

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
2.68	54.02

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	1.85	49.66	93.6	0.963	3.35	2.8		21161

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	1.85	1.98	91.9		0.401		2.87

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	1.85	49.66	21161	1102	93.529	0.181	0.1792	0.1896	0.2122	0.2164	18.776

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]
0.343			0.343		-0.685

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.253
r_dihedral_angle_4_deg	12.82
r_dihedral_angle_3_deg	10.554
r_dihedral_angle_1_deg	6.722
r_lrange_it	4.261
r_lrange_other	4.127
r_scangle_it	2.527
r_scangle_other	2.514
r_mcangle_other	1.948
r_mcangle_it	1.943

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.253
r_dihedral_angle_4_deg	12.82
r_dihedral_angle_3_deg	10.554
r_dihedral_angle_1_deg	6.722
r_lrange_it	4.261
r_lrange_other	4.127
r_scangle_it	2.527
r_scangle_other	2.514
r_mcangle_other	1.948
r_mcangle_it	1.943
r_scbond_it	1.612
r_scbond_other	1.541
r_angle_refined_deg	1.467
r_angle_other_deg	1.29
r_mcbond_it	1.216
r_mcbond_other	1.205
r_nbd_refined	0.189
r_symmetry_nbd_other	0.183
r_nbd_other	0.182
r_nbtor_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.149
r_xyhbond_nbd_refined	0.137
r_symmetry_nbtor_other	0.077
r_symmetry_nbd_refined	0.065
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_metal_ion_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1787
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms	10

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.