9TCZ | pdb_00009tcz

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
2.49	50.63

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		2024-02-03	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	2.06	48.12	100	0.995	6.63	12.8		15277

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	2.06	2.11	99.8		0.739

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	2.06	48.116	15277	775	99.98	0.19	0.1871	0.1992	0.2396	0.2471	33.493

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]
2.047			2.047		-4.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.854
r_dihedral_angle_4_deg	20.552
r_dihedral_angle_3_deg	11.039
r_dihedral_angle_1_deg	6.776
r_lrange_other	4.487
r_lrange_it	4.485
r_scangle_other	3.44
r_scangle_it	3.427
r_mcangle_it	2.655
r_mcangle_other	2.654

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.854
r_dihedral_angle_4_deg	20.552
r_dihedral_angle_3_deg	11.039
r_dihedral_angle_1_deg	6.776
r_lrange_other	4.487
r_lrange_it	4.485
r_scangle_other	3.44
r_scangle_it	3.427
r_mcangle_it	2.655
r_mcangle_other	2.654
r_scbond_other	2.476
r_scbond_it	2.474
r_mcbond_it	1.974
r_mcbond_other	1.972
r_angle_refined_deg	1.587
r_angle_other_deg	1.261
r_nbd_other	0.223
r_symmetry_xyhbond_nbd_refined	0.216
r_nbd_refined	0.195
r_symmetry_nbd_other	0.187
r_symmetry_nbd_refined	0.186
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.156
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.053
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	152
Heterogen Atoms	86

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.