Experiment: 9YUX

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, HANGING DROP		293	sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.91

Symmetry
Space Group	C 2 2 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		2024-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95373	Australian Synchrotron	MX2

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	1.57	47.48	99.5	1	11.1	6.5		52605

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	1.57	1.6			0.84

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	1.573	39.939	52587	2604	99.468	0.167	0.166	0.1792	0.1891	0.201	15.005

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]
1.065			-0.136		-0.929

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.441
r_dihedral_angle_3_deg	12.339
r_dihedral_angle_2_deg	9.173
r_dihedral_angle_1_deg	6.5
r_lrange_it	4.96
r_lrange_other	4.614
r_scangle_it	3.274
r_scangle_other	3.26
r_scbond_it	2.055
r_scbond_other	2.043

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.441
r_dihedral_angle_3_deg	12.339
r_dihedral_angle_2_deg	9.173
r_dihedral_angle_1_deg	6.5
r_lrange_it	4.96
r_lrange_other	4.614
r_scangle_it	3.274
r_scangle_other	3.26
r_scbond_it	2.055
r_scbond_other	2.043
r_mcangle_it	1.864
r_mcangle_other	1.864
r_angle_refined_deg	1.473
r_mcbond_it	1.189
r_mcbond_other	1.189
r_angle_other_deg	0.538
r_nbd_refined	0.207
r_symmetry_nbd_other	0.186
r_xyhbond_nbd_refined	0.18
r_nbd_other	0.176
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.135
r_symmetry_nbd_refined	0.082
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.076
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2529
Nucleic Acid Atoms
Solvent Atoms	448
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.

9YUX | pdb_00009yux