9T5E | pdb_00009t5e

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Y2E

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.1M PTCP, pH 8.0, 30% w/v PEG 1000

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.13

Symmetry
Space Group	P 21 21 21

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		2024-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

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	1.689	49.345	99.76	0.999	13.45	13.5		79239

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	1.69	1.75			0.999

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	MOLECULAR REPLACEMENT	FREE R-VALUE	1.689	49.345	79239	3903	99.721	0.211	0.2094	0.2196	0.2418	0.2474	28.176

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]
-1.895			2.702		-0.807

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.26
r_dihedral_angle_3_deg	13.216
r_dihedral_angle_1_deg	7.199
r_lrange_other	6.535
r_lrange_it	6.534
r_dihedral_angle_2_deg	6.087
r_scangle_it	5.134
r_scangle_other	5.134
r_mcangle_other	3.596
r_mcangle_it	3.595

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.26
r_dihedral_angle_3_deg	13.216
r_dihedral_angle_1_deg	7.199
r_lrange_other	6.535
r_lrange_it	6.534
r_dihedral_angle_2_deg	6.087
r_scangle_it	5.134
r_scangle_other	5.134
r_mcangle_other	3.596
r_mcangle_it	3.595
r_scbond_it	3.377
r_scbond_other	3.376
r_dihedral_angle_other_2_deg	3.092
r_mcbond_it	2.521
r_mcbond_other	2.52
r_angle_refined_deg	1.597
r_dihedral_angle_other_3_deg	1.336
r_angle_other_deg	0.561
r_nbd_refined	0.211
r_nbd_other	0.199
r_symmetry_nbd_other	0.197
r_symmetry_nbd_refined	0.19
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.134
r_symmetry_xyhbond_nbd_refined	0.096
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.079
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4673
Nucleic Acid Atoms
Solvent Atoms	309
Heterogen Atoms	78

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.