6D0G | pdb_00006d0g

1.78 Angstrom Resolution Crystal Structure of Quercetin 2,3-dioxygenase from Acinetobacter baumannii

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	292	8.0 mg/mL protein in 0.01 M Tris, pH 8.3, screen: PACT (F2) (0.2 M sodium bromide, 0.1 M Bis-Tris propane, pH 6.5, 20% w/v PEG3350)

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.883	α = 90
b = 73.616	β = 90
c = 202.741	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	RAYONIX MX-300	C(111)	2018-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.78	30	97.2	0.095	0.095	0.098	0.026	29.3	13.3		29760		-3	24.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.81	85.4		0.755	0.755	0.79	0.223	0.773	3.3	11.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.78	29.78	28236	1472	97.09	0.17629	0.17438	0.1831	0.21009	0.2178	RANDOM	30.645

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]
-1.37			0.53		0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.744
r_dihedral_angle_3_deg	10.153
r_dihedral_angle_4_deg	8.249
r_long_range_B_refined	5.251
r_long_range_B_other	5.156
r_dihedral_angle_1_deg	3.658
r_scangle_other	2.779
r_scbond_it	1.919
r_scbond_other	1.919
r_angle_refined_deg	1.509
r_mcangle_it	1.461
r_mcangle_other	1.461
r_mcbond_it	0.996
r_mcbond_other	0.988
r_angle_other_deg	0.847
r_chiral_restr	0.09
r_gen_planes_refined	0.021
r_gen_planes_other	0.018
r_bond_refined_d	0.008
r_bond_other_d	0.001
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	2357
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing