9T1Y | pdb_00009t1y

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JQK

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289.15	0.1M Tris pH 8.5, 22% v/v PEG smear broad (4.55% v/v PEG 400, 4.55% v/v PEG 500 MME, 4.55% v/v PEG 600, 4.55% w/v PEG 1000, 4.55% w/v PEG 2000, 4.55% w/v PEG 3350, 4.55% w/v PEG 4000, 4.55% w/v PEG 5000 MME, 4.55% w/v PEG 6000, 4.55% w/v PEG 8000, 4.55% w/v PEG 10000).

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.23

Symmetry
Space Group	C 1 2 1

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 EIGER2 XE 16M		2022-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97950	Diamond	I04

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	2.7	104.85	100	0.993	6	13.9		39892

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	2.7	2.81			0.662

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.7	104.853	39889	1970	100	0.208	0.2065	0.2102	0.2436	0.2179	RANDOM	70.815

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]
-4.251		-1.805	0.186		4.373

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.521
r_dihedral_angle_6_deg	13.799
r_dihedral_angle_2_deg	9.043
r_dihedral_angle_1_deg	7.417
r_lrange_it	6.557
r_lrange_other	6.556
r_mcangle_it	4.667
r_mcangle_other	4.667
r_scangle_it	4.62
r_scangle_other	4.619

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.521
r_dihedral_angle_6_deg	13.799
r_dihedral_angle_2_deg	9.043
r_dihedral_angle_1_deg	7.417
r_lrange_it	6.557
r_lrange_other	6.556
r_mcangle_it	4.667
r_mcangle_other	4.667
r_scangle_it	4.62
r_scangle_other	4.619
r_mcbond_it	2.882
r_mcbond_other	2.879
r_scbond_it	2.868
r_scbond_other	2.867
r_angle_refined_deg	1.401
r_dihedral_angle_other_2_deg	0.925
r_angle_other_deg	0.475
r_nbd_refined	0.212
r_symmetry_nbd_other	0.196
r_nbd_other	0.193
r_nbtor_refined	0.182
r_symmetry_nbd_refined	0.162
r_xyhbond_nbd_refined	0.138
r_ncsr_local_group_1	0.123
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_refined	0.069
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10429
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	4

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.