5YDB

Crystal structure of the complex of type II dehydroquinate dehydratase from Acinetobacter baumannii with dehydroquinic acid at 1.76 Angstrom resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.05M Cadmium sulfate hydrate, 0.1M HEPES, PH 7.5, IM Sodium acetate trihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.117	α = 90
b = 139.117	β = 90
c = 79.587	γ = 120

Symmetry
Space Group	H 3

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	MARRESEARCH	MIRROR	2017-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.97	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.76	69.56	98.3	8.2	2.8		56929

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.76	1.82	98.8		0.7	2.8

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5B6P	1.76	69.56	53283	2666	98.28	0.19926	0.19723	0.24766	RANDOM	48.171

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]
-0.4	-0.2		-0.4		1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.127
r_dihedral_angle_3_deg	17.45
r_dihedral_angle_4_deg	10.506
r_long_range_B_refined	9.909
r_long_range_B_other	9.909
r_dihedral_angle_1_deg	6.512
r_scangle_other	5.501
r_mcangle_it	4.832
r_mcangle_other	4.831
r_scbond_it	3.718
r_scbond_other	3.714
r_mcbond_it	3.128
r_mcbond_other	3.122
r_angle_refined_deg	2.153
r_angle_other_deg	1.222
r_chiral_restr	0.154
r_bond_refined_d	0.024
r_gen_planes_refined	0.013
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4484
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing