9TCY | pdb_00009tcy

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
2.55	51.83

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 16M		2024-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9763	MAX IV	BioMAX

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	1.84	44.42	100	0.994	6.29	12.3		21593

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	1.85	1.9	99.7		0.627

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	1.85	44.416	21593	1120	99.944	0.195	0.1924	0.2037	0.2383	0.2408	24.514

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]
0.984			0.984		-1.967

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.522
r_dihedral_angle_4_deg	13.361
r_dihedral_angle_3_deg	9.878
r_dihedral_angle_1_deg	7.382
r_lrange_other	4.633
r_lrange_it	4.629
r_scangle_it	2.762
r_scangle_other	2.761
r_scbond_it	2.031
r_scbond_other	2.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.522
r_dihedral_angle_4_deg	13.361
r_dihedral_angle_3_deg	9.878
r_dihedral_angle_1_deg	7.382
r_lrange_other	4.633
r_lrange_it	4.629
r_scangle_it	2.762
r_scangle_other	2.761
r_scbond_it	2.031
r_scbond_other	2.03
r_mcangle_other	1.966
r_mcangle_it	1.965
r_mcbond_it	1.591
r_angle_refined_deg	1.524
r_mcbond_other	1.506
r_angle_other_deg	1.333
r_symmetry_nbd_refined	0.294
r_nbd_other	0.263
r_nbd_refined	0.193
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.151
r_symmetry_xyhbond_nbd_refined	0.143
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.066
r_metal_ion_refined	0.028
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_symmetry_xyhbond_nbd_other	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1787
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	49

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.