9T5F | pdb_00009t5f

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	7.5	293	0.1M Sodium HEPES; MOPS (acid) pH7.5, 30% v/v 40% v/v PEG 500 MME; 20 % w/v PEG 200001, 0.12M Ethylene glycols

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.01

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		2025-10-09	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	1.68	45.97	95.95	0.999	14.42	13.4		80677

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	1.68	1.74			0.636

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	1.68	45.97	80677	3870	96.847	0.244	0.2427	0.2558	0.2647	0.2753	28.015

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]
-2.118			3.012		-0.894

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.708
r_dihedral_angle_3_deg	15.686
r_dihedral_angle_2_deg	7.671
r_dihedral_angle_1_deg	7.304
r_lrange_it	6.286
r_lrange_other	6.282
r_dihedral_angle_other_2_deg	5.398
r_scangle_it	4.607
r_scangle_other	4.606
r_mcangle_other	3.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.708
r_dihedral_angle_3_deg	15.686
r_dihedral_angle_2_deg	7.671
r_dihedral_angle_1_deg	7.304
r_lrange_it	6.286
r_lrange_other	6.282
r_dihedral_angle_other_2_deg	5.398
r_scangle_it	4.607
r_scangle_other	4.606
r_mcangle_other	3.63
r_mcangle_it	3.629
r_scbond_it	2.958
r_scbond_other	2.958
r_mcbond_it	2.452
r_mcbond_other	2.448
r_angle_refined_deg	1.482
r_dihedral_angle_other_3_deg	0.89
r_angle_other_deg	0.502
r_nbd_refined	0.211
r_symmetry_nbd_other	0.196
r_nbd_other	0.196
r_nbtor_refined	0.184
r_symmetry_nbd_refined	0.137
r_xyhbond_nbd_refined	0.133
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_refined	0.083
r_chiral_restr	0.069
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	4691
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	90

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.