Experiment: 9PL3

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4D7R

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	292	Protein: 12.9 mg/ml, 10mM HEPES (pH 7.2), 1mM TCEP, 2% Glycerol, 5mM Imidazole; Screen: PEGs II (F8), 0.1M Sodium acetate, 25% (w/v) PEG 4000, 8% (w/v) Isopropanol; Cryo: Reservoir.

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.6

Symmetry
Space Group	P 1 21 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 X 9M		2024-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.92020	NSLS-II	17-ID-1

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.95	30	99.8	0.2	0.2	0.089	0.984	8.8	5.8		72403		-3	17.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98	99.5		0.86	0.86	0.384	0.428	2.1	5.6

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 (Observed)	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	1.95	29.13	68623	3760	99.06	0.17424	0.17258	0.1838	0.20348	0.2222	RANDOM	21.565

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]
0.61		0.33	-19.85		19.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	5.735
r_long_range_B_refined	3.996
r_long_range_B_other	3.892
r_dihedral_angle_1_deg	2.624
r_scangle_other	1.669
r_dihedral_angle_2_deg	1.656
r_angle_refined_deg	1.463
r_mcangle_it	1.278
r_mcangle_other	1.278
r_scbond_it	1.037

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	5.735
r_long_range_B_refined	3.996
r_long_range_B_other	3.892
r_dihedral_angle_1_deg	2.624
r_scangle_other	1.669
r_dihedral_angle_2_deg	1.656
r_angle_refined_deg	1.463
r_mcangle_it	1.278
r_mcangle_other	1.278
r_scbond_it	1.037
r_scbond_other	1.037
r_mcbond_it	0.756
r_mcbond_other	0.756
r_angle_other_deg	0.507
r_chiral_restr	0.082
r_gen_planes_refined	0.013
r_gen_planes_other	0.01
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8116
Nucleic Acid Atoms
Solvent Atoms	604
Heterogen Atoms	24

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.

9PL3 | pdb_00009pl3