6D0P | pdb_00006d0p

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

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	292	8.5 mg/mL protein in 0.01 M Tris, pH 8.3, screen: Classics II (H1) (0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 8.5, 25% w/v PEG3350)

Crystal Properties
Matthews coefficient	Solvent content
2.86	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.481	α = 90
b = 131.977	β = 103.58
c = 123.987	γ = 90

Symmetry
Space Group	C 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	RAYONIX MX-300	C(111)	2018-03-14	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	1.88	30	99.9	0.094	0.094	0.107	0.05	15.7	4.5		120737		-3	24.4

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	1.88	1.91	100		0.763	0.763	0.865	0.404	0.649	2.1	4.4

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	1.88	29.81	114778	5945	99.8	0.15975	0.15821	0.1714	0.19039	0.1996	RANDOM	27.715

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]
0.03		-0.41	0.33		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.251
r_sphericity_bonded	31.152
r_sphericity_free	21.502
r_dihedral_angle_4_deg	10.707
r_dihedral_angle_3_deg	9.89
r_long_range_B_refined	6.436
r_long_range_B_other	6.285
r_dihedral_angle_1_deg	4.323
r_scangle_other	3.772
r_scbond_it	2.428
r_scbond_other	2.428
r_mcangle_it	2.081
r_mcangle_other	2.081
r_mcbond_it	1.384
r_mcbond_other	1.383
r_angle_refined_deg	1.34
r_angle_other_deg	0.432
r_chiral_restr	0.058
r_gen_planes_refined	0.02
r_gen_planes_other	0.017
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8912
Nucleic Acid Atoms
Solvent Atoms	1056
Heterogen Atoms	101

Software

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