2IGA | pdb_00002iga

Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations.

X-RAY DIFFRACTION

---

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		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, pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.678	α = 90
b = 153.022	β = 90
c = 96.389	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		2006-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2		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	1.95	52.7	87.8	0.095	5.4	2.08		105058

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	1.95	2.02	91.6		0.379	1.9	2.16

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1F1X	1.95	52.7	104994	104994	5277	87.8	0.185	0.19	0.245	0.25	32.59

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					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.727
r_dihedral_angle_4_deg	18.432
r_dihedral_angle_3_deg	14.294
r_dihedral_angle_1_deg	7.34
r_scangle_it	3.467
r_scbond_it	2.55
r_angle_refined_deg	1.671
r_mcangle_it	1.36
r_mcbond_it	1.112
r_nbtor_refined	0.308
r_nbd_refined	0.21
r_symmetry_metal_ion_refined	0.195
r_symmetry_vdw_refined	0.177
r_xyhbond_nbd_refined	0.162
r_symmetry_hbond_refined	0.144
r_chiral_restr	0.122
r_metal_ion_refined	0.096
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11600
Nucleic Acid Atoms
Solvent Atoms	1042
Heterogen Atoms	139

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
CCP4	phasing