9TD8 | pdb_00009td8

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
2.57	52.12

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	1.7	48.727	100	0.994	6.3	13.4		28034

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	1.7	1.76	100		0.553		11

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	1.7	48.727	27987	1397	99.971	0.185	0.1832	0.1947	0.2233	0.2283	21.089

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]
0.682			0.682		-1.363

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.765
r_dihedral_angle_4_deg	17.641
r_dihedral_angle_3_deg	10.759
r_dihedral_angle_1_deg	7.252
r_lrange_it	5.993
r_lrange_other	5.473
r_scangle_it	3.005
r_scangle_other	2.48
r_scbond_it	2.319
r_mcangle_other	1.852

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.765
r_dihedral_angle_4_deg	17.641
r_dihedral_angle_3_deg	10.759
r_dihedral_angle_1_deg	7.252
r_lrange_it	5.993
r_lrange_other	5.473
r_scangle_it	3.005
r_scangle_other	2.48
r_scbond_it	2.319
r_mcangle_other	1.852
r_mcangle_it	1.851
r_scbond_other	1.844
r_angle_refined_deg	1.52
r_mcbond_it	1.462
r_mcbond_other	1.413
r_angle_other_deg	1.395
r_metal_ion_refined	0.414
r_nbd_other	0.284
r_symmetry_nbd_refined	0.255
r_nbd_refined	0.221
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.145
r_symmetry_xyhbond_nbd_refined	0.119
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.076
r_symmetry_xyhbond_nbd_other	0.041
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
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	348
Heterogen Atoms	71

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.