2IG9

Structure of a full-length Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in a new spacegroup.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F1X	PDB entry 1F1X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	292	18% PEG8000, 0.2 M calcium acetate, 0.1 M sodium cacodylate. Prior to freezing in liquid nitrogen, crystals were sequentially transferred into mother liquor solutions containing 5, 10, 15, and then 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.29	45.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.445	α = 90
b = 152.802	β = 90
c = 99.714	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	NOIR-1		2005-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.23983	ALS	4.2.2

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	1.9	53.15	99.8	0.099	7.1	3.18	133141	132886

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	1.9	1.97	99.9		0.532	2	3.1	13150

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 1F1X	1.9	46.08	132683	132683	6680	99.67	0.18976	0.1874	0.23443	RANDOM	23.337

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]
0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.881
r_dihedral_angle_4_deg	17.693
r_dihedral_angle_3_deg	13.19
r_dihedral_angle_1_deg	7.036
r_scangle_it	3.065
r_scbond_it	2.084
r_angle_refined_deg	1.455
r_mcangle_it	1.166
r_mcbond_it	0.956
r_nbtor_refined	0.305
r_symmetry_hbond_refined	0.223
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.189
r_symmetry_metal_ion_refined	0.165
r_xyhbond_nbd_refined	0.148
r_metal_ion_refined	0.105
r_chiral_restr	0.103
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11600
Nucleic Acid Atoms
Solvent Atoms	1248
Heterogen Atoms	75

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
d*TREK	data reduction
d*TREK	data scaling
CCP4	phasing