9TD9 | pdb_00009td9

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
2.56	51.87

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	0.551	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	1.493	48.623	94.1	0.996	5.1	13.7		38557

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	1.493	1.52	84.1		0.5		13.2

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	1.493	48.623	38557	1901	94.019	0.172	0.17	0.1792	0.2065	0.2104	16.157

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]
0.416			0.416		-0.831

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.87
r_dihedral_angle_4_deg	14.42
r_dihedral_angle_3_deg	10.29
r_dihedral_angle_1_deg	7.111
r_lrange_it	5.885
r_lrange_other	5.564
r_scangle_it	2.598
r_scangle_other	2.298
r_scbond_it	1.993
r_scbond_other	1.646

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.87
r_dihedral_angle_4_deg	14.42
r_dihedral_angle_3_deg	10.29
r_dihedral_angle_1_deg	7.111
r_lrange_it	5.885
r_lrange_other	5.564
r_scangle_it	2.598
r_scangle_other	2.298
r_scbond_it	1.993
r_scbond_other	1.646
r_angle_refined_deg	1.605
r_angle_other_deg	1.467
r_mcangle_it	1.408
r_mcangle_other	1.408
r_mcbond_it	1.124
r_mcbond_other	0.991
r_nbd_refined	0.228
r_symmetry_nbd_refined	0.222
r_nbd_other	0.218
r_symmetry_xyhbond_nbd_refined	0.214
r_symmetry_nbd_other	0.205
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.143
r_metal_ion_refined	0.104
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.077
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
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	356
Heterogen Atoms	79

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.