4UIO | pdb_00004uio

Structure of the Salmonella typhi Type I Dehydroquinase covalently inhibited by a 3-dehydroquinic acid derivative

X-RAY DIFFRACTION

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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		5.5		25% (W/V) PEG 3350, 0.1 M BIS-TRIS PH 5.5, 0.2 M MAGNESIUM CHLORIDE

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.399	α = 90
b = 42.327	β = 105.13
c = 84.828	γ = 90

Symmetry
Space Group	I 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	CCD	ADSC QUANTUM 315r	MIRRORS	2014-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A		ESRF	BM30A

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	1.35	45.48	99.3	0.07	12.8	3.6		50525		-3	8

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	1.35	1.42	99.3		0.4	3.5	3.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1QFE	1.35	37.63	48464	2060	99.26	0.17525	0.1736	0.18	0.21413	0.22	RANDOM	8.938

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]
0.69		-0.66	-0.09		-0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.435
r_sphericity_free	22.789
r_dihedral_angle_4_deg	15.669
r_dihedral_angle_3_deg	13.173
r_dihedral_angle_1_deg	5.558
r_sphericity_bonded	5.543
r_rigid_bond_restr	1.81
r_angle_refined_deg	1.469
r_mcangle_it	1.469
r_angle_other_deg	0.908
r_xyhbond_nbd_other	0.585
r_symmetry_hbond_other	0.517
r_symmetry_vdw_refined	0.321
r_symmetry_hbond_refined	0.275
r_nbd_refined	0.273
r_symmetry_vdw_other	0.268
r_nbd_other	0.184
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.087
r_nbtor_other	0.086
r_bond_refined_d	0.01
r_mcbond_it	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_mcbond_other	0.002
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	1919
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	18

Software

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