6C5C

Crystal structure of the 3-dehydroquinate synthase (DHQS) domain of Aro1 from Candida albicans SC5314 in complex with NADH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SG6	PDB entry 1SG6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.2 M sodium thiocyanate, 20% PEG3350, 2 mM NADH, 0.5 mM zinc chloride, cryoprotectant: 8% glycerol, 8% ethylene glycol, 8% sucrose

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.678	α = 90
b = 92.06	β = 97.57
c = 88.915	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	CCD	ADSC QUANTUM 210r	mirrors	2017-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9793	APS	19-BM

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	1.85	30	99.9	0.045	37.8	4.8		69649		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.88	100		0.956	0.717	1.44	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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1SG6	1.85	30	66446	2108	99.26	0.17695	0.17606	0.203	RANDOM	41.338

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]
3		1.23	-1.3		-1.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.441
r_dihedral_angle_4_deg	15.611
r_dihedral_angle_3_deg	14.11
r_dihedral_angle_1_deg	5.702
r_long_range_B_refined	5.392
r_long_range_B_other	5.392
r_angle_refined_deg	1.655
r_scangle_other	1.374
r_angle_other_deg	0.99
r_mcangle_it	0.939
r_mcangle_other	0.939
r_scbond_it	0.931
r_scbond_other	0.929
r_mcbond_it	0.602
r_mcbond_other	0.601
r_chiral_restr	0.094
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
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	5908
Nucleic Acid Atoms
Solvent Atoms	389
Heterogen Atoms	141

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
SBC-Collect	data collection