5WRF

Crystal structure of dodecameric type II dehydroquinate dehydratase from Acinetobacter baumannii with unexplained connecting electron density between free cysteine residues of molecular pairs

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RHC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	30% PEG3350, MgSO4, Tris buffer

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.801	α = 90
b = 135.75	β = 97.53
c = 142.74	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	MARRESEARCH		2016-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.51	37.75	95.3	0.084	13.4	3.5		63061

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	2.51	2.54	94.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4RHC	2.51	37.75	58540	1159	94.67	0.21002	0.20915	0.25588	RANDOM	54.63

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]
-2.35		-0.73	1.71		0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.427
r_dihedral_angle_3_deg	19.174
r_dihedral_angle_4_deg	17.463
r_long_range_B_refined	11.094
r_long_range_B_other	11.094
r_dihedral_angle_1_deg	7.266
r_mcangle_it	6.744
r_mcangle_other	6.744
r_scangle_other	6.569
r_mcbond_it	4.307
r_mcbond_other	4.305
r_scbond_it	4.171
r_scbond_other	4.171
r_angle_other_deg	3.438
r_angle_refined_deg	2.094
r_chiral_restr	0.134
r_bond_other_d	0.028
r_gen_planes_other	0.022
r_gen_planes_refined	0.02
r_bond_refined_d	0.019
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	13440
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	4

Software

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