Experiment: 9YUU

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
2.6	52.74

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		2024-04-26	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	1.45	47.48	99.9	1	15	6.8		71275

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	1.45	1.47			0.81

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	1.45	47.48	66974	3379	99.846	0.128	0.1263	0.1262	0.1603	0.1602	18.129

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]
1.164			-0.393		-0.771

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.003
r_lrange_it	15.928
r_lrange_other	13.744
r_dihedral_angle_3_deg	12.003
r_scangle_it	8.959
r_scangle_other	8.787
r_dihedral_angle_2_deg	8.655
r_mcangle_it	6.603
r_mcangle_other	6.603
r_dihedral_angle_1_deg	6.247

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.003
r_lrange_it	15.928
r_lrange_other	13.744
r_dihedral_angle_3_deg	12.003
r_scangle_it	8.959
r_scangle_other	8.787
r_dihedral_angle_2_deg	8.655
r_mcangle_it	6.603
r_mcangle_other	6.603
r_dihedral_angle_1_deg	6.247
r_scbond_it	6.023
r_scbond_other	5.882
r_mcbond_it	4.293
r_mcbond_other	4.288
r_rigid_bond_restr	2.908
r_angle_refined_deg	1.593
r_angle_other_deg	0.594
r_nbd_other	0.263
r_nbd_refined	0.233
r_symmetry_nbd_other	0.195
r_xyhbond_nbd_refined	0.188
r_symmetry_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.177
r_xyhbond_nbd_other	0.131
r_symmetry_nbd_refined	0.129
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.038
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2534
Nucleic Acid Atoms
Solvent Atoms	427
Heterogen Atoms	30

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.

9YUU | pdb_00009yuu