9TD6 | pdb_00009td6

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	51.97

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	2.22	48.691	100	0.985	2.4	11.5		12572

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	2.22	2.3	99.9		0.628

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	2.22	48.691	12542	630	99.888	0.216	0.2153	0.2206	0.2366	0.2433	34.254

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]
0.033			0.033		-0.067

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.374
r_dihedral_angle_4_deg	15.967
r_dihedral_angle_3_deg	12.495
r_dihedral_angle_1_deg	7.844
r_lrange_other	7.223
r_lrange_it	7.221
r_scangle_it	4.205
r_scangle_other	4.203
r_mcangle_other	3.567
r_mcangle_it	3.565

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.374
r_dihedral_angle_4_deg	15.967
r_dihedral_angle_3_deg	12.495
r_dihedral_angle_1_deg	7.844
r_lrange_other	7.223
r_lrange_it	7.221
r_scangle_it	4.205
r_scangle_other	4.203
r_mcangle_other	3.567
r_mcangle_it	3.565
r_scbond_it	3.353
r_scbond_other	3.351
r_mcbond_it	2.445
r_mcbond_other	2.291
r_angle_refined_deg	1.514
r_angle_other_deg	1.224
r_nbd_other	0.212
r_symmetry_nbd_other	0.198
r_nbd_refined	0.196
r_symmetry_xyhbond_nbd_refined	0.165
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.164
r_symmetry_nbd_refined	0.159
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.059
r_metal_ion_refined	0.031
r_bond_refined_d	0.007
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	128
Heterogen Atoms	118

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.