9TCV | pdb_00009tcv

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
2.66	53.68

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		2023-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8731	ESRF	ID23-2

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	1.85	109.62	99.5	0.995	8.1	13.6		22367

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	1.89			0.748

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	49.472	22262	1156	99.043	0.195	0.1936	0.2052	0.2277	0.2346	25.497

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]
1.22			1.22		-2.441

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.781
r_dihedral_angle_4_deg	12.644
r_dihedral_angle_3_deg	11.137
r_dihedral_angle_1_deg	7.22
r_lrange_it	5.176
r_lrange_other	4.862
r_scangle_it	3.075
r_scangle_other	3.046
r_scbond_it	2.208
r_mcangle_it	2.202

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.781
r_dihedral_angle_4_deg	12.644
r_dihedral_angle_3_deg	11.137
r_dihedral_angle_1_deg	7.22
r_lrange_it	5.176
r_lrange_other	4.862
r_scangle_it	3.075
r_scangle_other	3.046
r_scbond_it	2.208
r_mcangle_it	2.202
r_mcangle_other	2.202
r_scbond_other	2.193
r_mcbond_it	1.854
r_mcbond_other	1.717
r_angle_refined_deg	1.509
r_angle_other_deg	1.329
r_symmetry_nbd_refined	0.236
r_nbd_refined	0.208
r_nbd_other	0.208
r_symmetry_nbd_other	0.19
r_xyhbond_nbd_refined	0.162
r_nbtor_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.157
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.065
r_metal_ion_refined	0.012
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
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	311
Heterogen Atoms	27

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.