9TDK | pdb_00009tdk

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
2.63	53.3

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	1.65	44.953	99.8	0.994	3.7	14		31311

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	1.65	1.71	99.7		0.638		13.7

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	1.65	44.953	31277	1567	99.735	0.169	0.168	0.1807	0.1908	0.1984	14.96

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]
0.125			0.125		-0.249

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.884
r_dihedral_angle_4_deg	19.853
r_dihedral_angle_3_deg	11.498
r_dihedral_angle_1_deg	6.604
r_lrange_it	4.834
r_lrange_other	4.694
r_scangle_it	2.866
r_scangle_other	2.851
r_mcangle_other	1.909
r_mcangle_it	1.904

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.884
r_dihedral_angle_4_deg	19.853
r_dihedral_angle_3_deg	11.498
r_dihedral_angle_1_deg	6.604
r_lrange_it	4.834
r_lrange_other	4.694
r_scangle_it	2.866
r_scangle_other	2.851
r_mcangle_other	1.909
r_mcangle_it	1.904
r_scbond_it	1.878
r_scbond_other	1.852
r_angle_refined_deg	1.553
r_angle_other_deg	1.38
r_mcbond_it	1.227
r_mcbond_other	1.164
r_nbd_refined	0.194
r_symmetry_nbd_other	0.186
r_nbd_other	0.175
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_refined	0.146
r_metal_ion_refined	0.09
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.072
r_symmetry_nbd_refined	0.07
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
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	210
Heterogen Atoms	61

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.