8B2A

Crystal structure of type I dehydroquinase from Salmonella typhi inhibited by an epoxide derivative

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	20% (w/v) PEG 3350, 0.1 M Bis-Tris-HCl, 0.2 M lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.2	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.382	α = 90
b = 79.574	β = 101.171
c = 83.535	γ = 90

Symmetry
Space Group	P 1 2 1

Diffraction

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 PILATUS 6M		2020-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.65	81.95	98	0.027	0.032	0.017	1	19.1	3.4		54904			37.3495

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.74	97.7		0.323	0.381	0.202	0.953	3.4	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6SFH	1.65	79.701	54904	2771	97.769	0.221	0.2193	0.255	32.147

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]
-1.026		-1.376	3.294		-1.599

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.941
r_dihedral_angle_4_deg	15.842
r_dihedral_angle_3_deg	13.022
r_dihedral_angle_1_deg	6.744
r_lrange_other	5.767
r_lrange_it	5.766
r_scangle_it	4.395
r_scangle_other	4.39
r_mcangle_other	3.352
r_mcangle_it	3.35
r_scbond_it	2.967
r_scbond_other	2.962
r_mcbond_it	2.456
r_mcbond_other	2.444
r_angle_refined_deg	1.503
r_angle_other_deg	1.309
r_symmetry_xyhbond_nbd_refined	0.393
r_nbd_other	0.233
r_nbd_refined	0.214
r_symmetry_nbd_refined	0.187
r_symmetry_xyhbond_nbd_other	0.184
r_xyhbond_nbd_refined	0.18
r_symmetry_nbd_other	0.173
r_nbtor_refined	0.157
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.066
r_chiral_restr_other	0.016
r_bond_refined_d	0.008
r_gen_planes_refined	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	3704
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing