3OJK | pdb_00003ojk

Structure of Co-substituted Homoprotocatechuate 2,3-Dioxygenase in complex with 4-nitrocatechol at 1.68 Ang resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	13% PEG6000, 0.1 M calcium chloride, 0.1 M Tris-HCl. Cryoprotectant 25% PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.102	α = 90
b = 150.395	β = 90
c = 95.941	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	ADSC QUANTUM 315r		2010-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.9801	SOLEIL	PROXIMA 1

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	1.68	41.19	97.2	0.053	10.6	5.8	180226	175180		3	18.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.68	1.77	91.7		0.346	0.742	2.1	4.8	23848

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2IG9	1.68	37.96	166376	8696	96.67	0.15443	0.153	0.17	0.18153	0.2	RANDOM	20.873

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		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.183
r_dihedral_angle_4_deg	18.926
r_dihedral_angle_3_deg	12.729
r_dihedral_angle_1_deg	7.023
r_scangle_it	3.113
r_scbond_it	2.015
r_angle_refined_deg	1.46
r_mcangle_it	1.147
r_angle_other_deg	0.911
r_mcbond_it	0.696
r_mcbond_other	0.239
r_chiral_restr	0.096
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11512
Nucleic Acid Atoms
Solvent Atoms	1369
Heterogen Atoms	176

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
SCALA	data scaling