9UP3 | pdb_00009up3

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.15 M Cesium chloride, 15% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.49

Symmetry
Space Group	P 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 EIGER X 9M		2023-12-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.97915	SSRF	BL10U2

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	2.04	46.61	98.1	0.978	3.3	1.8		44381

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	2.04	2.09	96.8		0.393

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	2.04	46.6	44369	2083	98.09	0.231	0.2296	0.2343	0.2573	0.2635	51.397

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]
0.022	-0.049	0.014	-0.009	0.012	-0.041

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.778
r_lrange_other	11.153
r_lrange_it	11.14
r_scangle_it	8.574
r_scangle_other	8.572
r_dihedral_angle_6_deg	8.236
r_mcangle_it	5.767
r_mcangle_other	5.767
r_scbond_it	5.412
r_scbond_other	5.412

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.778
r_lrange_other	11.153
r_lrange_it	11.14
r_scangle_it	8.574
r_scangle_other	8.572
r_dihedral_angle_6_deg	8.236
r_mcangle_it	5.767
r_mcangle_other	5.767
r_scbond_it	5.412
r_scbond_other	5.412
r_dihedral_angle_1_deg	4.226
r_mcbond_it	4.133
r_mcbond_other	4.13
r_dihedral_angle_2_deg	1.665
r_angle_refined_deg	0.716
r_angle_other_deg	0.285
r_nbd_refined	0.2
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.163
r_nbd_other	0.14
r_symmetry_nbd_refined	0.136
r_xyhbond_nbd_refined	0.125
r_symmetry_nbtor_other	0.067
r_symmetry_xyhbond_nbd_refined	0.051
r_chiral_restr_other	0.046
r_chiral_restr	0.041
r_symmetry_xyhbond_nbd_other	0.034
r_gen_planes_refined	0.009
r_bond_refined_d	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4217
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms

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.