8SUU

Crystal structure of YisK from Bacillus subtilis in apo form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other	Other		Phyre homology model

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
2.47	50.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.937	α = 90
b = 93.768	β = 90
c = 125.484	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		2019-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97	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	2.26	46.93	100	0.117	0.07	0.998	11.9	6.3		30609

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	2.26	2.32			2.209	1.423	0.298

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	2.26	46.93	28549	1995	99.92	0.21376	0.21094	0.25478	RANDOM	64.315

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]
-0.99			1.34		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.401
r_dihedral_angle_1_deg	8.109
r_long_range_B_refined	5.273
r_long_range_B_other	5.271
r_scangle_other	3.398
r_mcangle_it	2.889
r_mcangle_other	2.888
r_scbond_other	2.09
r_scbond_it	2.089
r_mcbond_it	1.77
r_mcbond_other	1.77
r_angle_refined_deg	1.141
r_angle_other_deg	0.385
r_chiral_restr	0.055
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4502
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	2

Software

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