8B2C

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	7	291	26 % (w/v) PEG 2000 MME, 0.1 M HEPES-NaOH

Crystal Properties
Matthews coefficient	Solvent content
1.9	36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.713	α = 90
b = 47.08	β = 90
c = 105.2	γ = 90

Symmetry
Space Group	P 2 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	100	PIXEL	DECTRIS PILATUS 6M		2015-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	1.00556	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	1.55	105.2	89.4	0.036	0.041	0.019	1	22.6	4.1		28123			13.361

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	1.55	1.63	73.4		0.398	0.452	0.209	0.903	3.4	3.8

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	4CNN	1.55	52.6	27996	1366	88.595	0.168	0.1668	0.1997	16.196

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]
-0.236			-0.358		0.594

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.77
r_dihedral_angle_4_deg	20.107
r_dihedral_angle_3_deg	13.299
r_dihedral_angle_1_deg	6.647
r_lrange_it	4.484
r_lrange_other	4.455
r_scangle_it	3.604
r_scangle_other	3.554
r_scbond_it	2.421
r_scbond_other	2.338
r_mcangle_other	2.13
r_mcangle_it	2.119
r_angle_refined_deg	1.758
r_angle_other_deg	1.52
r_mcbond_it	1.426
r_mcbond_other	1.358
r_nbd_refined	0.221
r_symmetry_nbd_refined	0.218
r_nbd_other	0.211
r_symmetry_nbd_other	0.173
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.154
r_xyhbond_nbd_refined	0.146
r_xyhbond_nbd_other	0.094
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.082
r_chiral_restr_other	0.024
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_symmetry_xyhbond_nbd_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1936
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	38

Software

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