4CLM

Structure of Salmonella typhi type I dehydroquinase irreversibly inhibited with a 1,3,4-trihydroxyciclohexane-1-carboxylic acid derivative

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QFE	PDB ENTRY 1QFE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6		34% PEG 4000, 0.1 M CITRATE-PHOSPHATE PH 5.6

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.59	α = 90
b = 44.47	β = 95.17
c = 84.98	γ = 90

Symmetry
Space Group	P 1 21 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	PLANE-ELLIPSOIDAL MIRRORS (SI, RH, IR)	2013-03-08	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.4	47.17	96	0.06	12.8	3.6		85495		-3	9.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.48	76.1		0.22	4.1	2.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1QFE	1.4	47.21	81186	4293	95.95	0.12168	0.1199	0.15498	RANDOM	12.231

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]
0.16		-0.47	0.69		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.369
r_sphericity_free	28.717
r_dihedral_angle_4_deg	15.135
r_dihedral_angle_3_deg	13.353
r_scbond_it	8.568
r_sphericity_bonded	7.921
r_mcangle_it	7.551
r_mcbond_it	5.7767
r_dihedral_angle_1_deg	5.678
r_scangle_it	4.247
r_mcbond_other	2.2897
r_rigid_bond_restr	1.847
r_angle_refined_deg	1.533
r_angle_other_deg	0.947
r_symmetry_vdw_refined	0.287
r_nbd_refined	0.284
r_symmetry_hbond_refined	0.2645
r_symmetry_vdw_other	0.243
r_nbtor_refined	0.172
r_nbd_other	0.171
r_xyhbond_nbd_refined	0.163
r_metal_ion_refined	0.151
r_xyhbond_nbd_other	0.119
r_chiral_restr	0.091
r_nbtor_other	0.083
r_symmetry_hbond_other	0.071
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_metal_ion_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3790
Nucleic Acid Atoms
Solvent Atoms	665
Heterogen Atoms	17

Software

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