28JK | pdb_000028jk

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	100 mM MES, pH 6, 17 % w/v Polyethylene glycol 4000, 150 mM Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.42

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	Kirkpatrick-Baez mirror pair	2023-05-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.92	MAX IV	BioMAX

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.29	49.275	99.8	0.089	0.999	19.9	13.4		84773			54.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.29	2.33			1.5	0.621	1.6

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	2.44	49.275	70610	3539	99.943	0.175	0.1736	0.1831	0.2068	0.2149	71.548

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]
-5.077			3.257		1.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.965
r_dihedral_angle_3_deg	13.479
r_lrange_it	7.317
r_lrange_other	7.31
r_dihedral_angle_2_deg	7.214
r_dihedral_angle_1_deg	5.953
r_scangle_it	5.722
r_scangle_other	5.662
r_scbond_it	3.8
r_scbond_other	3.751

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.965
r_dihedral_angle_3_deg	13.479
r_lrange_it	7.317
r_lrange_other	7.31
r_dihedral_angle_2_deg	7.214
r_dihedral_angle_1_deg	5.953
r_scangle_it	5.722
r_scangle_other	5.662
r_scbond_it	3.8
r_scbond_other	3.751
r_mcangle_it	3.721
r_mcangle_other	3.721
r_mcbond_it	2.552
r_mcbond_other	2.552
r_chiral_restr_other	2.141
r_angle_refined_deg	1.435
r_dihedral_angle_other_2_deg	1.418
r_angle_other_deg	0.669
r_nbd_other	0.238
r_nbd_refined	0.216
r_symmetry_xyhbond_nbd_refined	0.216
r_symmetry_nbd_refined	0.199
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.132
r_ncsr_local_group_1	0.086
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.073
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10979
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	223

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.