8SUT

Crystal structure of YisK from Bacillus subtilis in complex with reaction product 4-Hydroxy-2-oxoglutaric acid

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	0.2 M Mg-acetate and 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.686	α = 90
b = 93.983	β = 90
c = 124.981	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	PIXEL	DECTRIS PILATUS3 6M		2019-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97934	APS	23-ID-B

Data Collection

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	1.93	47.04	98.2	0.068	0.035	0.998	12.4	4.6		47426

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	1.93	1.98			1.5	0.921	0.259

Refinement

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.93	47.04	45270	1998	97.7	0.18491	0.18295	0.2299	RANDOM	46.623

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]
1.7			-0.79		-0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.943
r_long_range_B_other	12.895
r_long_range_B_refined	12.876
r_scangle_other	11.265
r_scbond_it	8.418
r_scbond_other	8.37
r_dihedral_angle_1_deg	8.138
r_mcangle_it	6.952
r_mcangle_other	6.952
r_mcbond_it	5.694

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.943
r_long_range_B_other	12.895
r_long_range_B_refined	12.876
r_scangle_other	11.265
r_scbond_it	8.418
r_scbond_other	8.37
r_dihedral_angle_1_deg	8.138
r_mcangle_it	6.952
r_mcangle_other	6.952
r_mcbond_it	5.694
r_mcbond_other	5.694
r_angle_refined_deg	1.36
r_angle_other_deg	0.454
r_chiral_restr	0.067
r_bond_refined_d	0.014
r_gen_planes_refined	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	4662
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

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 R01GM133198.