28JJ | pdb_000028jj

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	125 mM MES, pH 6; 17 %w/v Polyethylene glycol 4000; 175 mM Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.65

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	Bruker PHOTON II	Helios multilayer	2020-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER X8 PROTEUM	1.5418

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.1	64.798	99.9	0.291	0.06	0.993	11.6	24		110584		1	27

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	99.2		2.4	0.773	0.198	1.1	10.2

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	2.3	64.798	84461	4221	99.844	0.222	0.2205	0.2246	0.2469	0.2486	44.576

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]
-0.494			2.322		-1.829

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.745
r_dihedral_angle_3_deg	13.585
r_dihedral_angle_2_deg	7.61
r_dihedral_angle_1_deg	6.056
r_lrange_it	3.784
r_lrange_other	3.772
r_chiral_restr_other	2.015
r_scangle_it	1.77
r_dihedral_angle_other_2_deg	1.723
r_scangle_other	1.703

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.745
r_dihedral_angle_3_deg	13.585
r_dihedral_angle_2_deg	7.61
r_dihedral_angle_1_deg	6.056
r_lrange_it	3.784
r_lrange_other	3.772
r_chiral_restr_other	2.015
r_scangle_it	1.77
r_dihedral_angle_other_2_deg	1.723
r_scangle_other	1.703
r_angle_refined_deg	1.457
r_mcangle_it	1.117
r_mcangle_other	1.117
r_scbond_it	1.109
r_scbond_other	1.068
r_angle_other_deg	0.642
r_mcbond_it	0.638
r_mcbond_other	0.638
r_symmetry_nbd_refined	0.238
r_nbd_other	0.219
r_nbd_refined	0.215
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.166
r_xyhbond_nbd_refined	0.153
r_ncsr_local_group_1	0.092
r_symmetry_nbtor_other	0.076
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	10915
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	228

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.