9TDB | pdb_00009tdb

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
2.51	51.06

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	1.989	48.222	99.7	0.994	7.9	13.9		17110

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	1.989	2.04	97.1		0.571		14.1

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	1.989	48.222	17071	865	99.58	0.184	0.1821	0.1906	0.2242	0.2272	32.432

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]
1.09			1.09		-2.179

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.742
r_dihedral_angle_4_deg	18.09
r_dihedral_angle_3_deg	12.385
r_dihedral_angle_1_deg	7.114
r_lrange_it	6.045
r_lrange_other	6.044
r_scangle_it	3.624
r_scangle_other	3.623
r_mcangle_it	2.771
r_mcangle_other	2.771

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.742
r_dihedral_angle_4_deg	18.09
r_dihedral_angle_3_deg	12.385
r_dihedral_angle_1_deg	7.114
r_lrange_it	6.045
r_lrange_other	6.044
r_scangle_it	3.624
r_scangle_other	3.623
r_mcangle_it	2.771
r_mcangle_other	2.771
r_scbond_it	2.672
r_scbond_other	2.671
r_mcbond_it	2.074
r_mcbond_other	2.059
r_angle_refined_deg	1.554
r_angle_other_deg	1.258
r_nbd_other	0.237
r_symmetry_xyhbond_nbd_refined	0.207
r_nbd_refined	0.196
r_symmetry_nbd_other	0.187
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.159
r_symmetry_nbd_refined	0.156
r_metal_ion_refined	0.082
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
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	106
Heterogen Atoms	108

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.