3ECK | pdb_00003eck

Structure of E323L Homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum in complex with putative O-O bond cleavage intermediate formed via in crystallo reaction with 4-sulfonyl catechol at low oxygen concentrations

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IG9	PDB ID 2IG9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	292	18% PEG8000, 0.1M Ca acetate, 0.1M Na cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.735	α = 90
b = 163.176	β = 90
c = 101.373	γ = 90

Symmetry
Space Group	P 21 21 2

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	SBC-3		2007-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97903	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.6	55	92.4	0.052	0.052	19.22	4.1	240583	222399		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66	73.2		0.342	3.067	3.3	17442

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ID 2IG9	1.6	24.2	211226	11135	92.41	0.17521	0.17401	0.17	0.19767	RANDOM	19.045

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.277
r_dihedral_angle_4_deg	16.866
r_dihedral_angle_3_deg	12.249
r_dihedral_angle_1_deg	6.704
r_scangle_it	2.715
r_scbond_it	1.769
r_angle_refined_deg	1.297
r_mcangle_it	1.078
r_mcbond_it	0.7
r_nbtor_refined	0.304
r_nbd_refined	0.2
r_symmetry_hbond_refined	0.197
r_symmetry_vdw_refined	0.177
r_metal_ion_refined	0.118
r_xyhbond_nbd_refined	0.11
r_symmetry_metal_ion_refined	0.097
r_chiral_restr	0.095
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11596
Nucleic Acid Atoms
Solvent Atoms	1393
Heterogen Atoms	71

Software

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