3OJT | pdb_00003ojt

Structure of native Fe-containing Homoprotocatechuate 2,3-Dioxygenase at 1.70 Ang resolution

X-RAY DIFFRACTION

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, 0.125 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
2.42	49.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.747	α = 90
b = 151.229	β = 90
c = 96.385	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	PIXEL	PSI PILATUS 6M		2010-05-15	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315r		2010-03-21	M
3	1	x-ray	100	CCD	ADSC QUANTUM 315r		2010-03-21	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9999	SLS	X10SA
2	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	1.7394	SOLEIL	PROXIMA 1
3	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	1.7428	SOLEIL	PROXIMA 1

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
1,2,3	1.7	89.43	98.3	0.064	0.104	8.6	3.4	177378	174363		3	18.3

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)
	1.7	1.79	98.6		0.427	0.682	2	3.3	25338

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	1.7	59.49	165298	8613	97.86	0.16099	0.15957	0.18	0.18796	0.2	RANDOM	20.596

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]
0.02			-0.04		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.953
r_dihedral_angle_4_deg	17.982
r_dihedral_angle_3_deg	12.739
r_dihedral_angle_1_deg	6.935
r_scangle_it	3.585
r_scbond_it	2.275
r_angle_refined_deg	1.461
r_mcangle_it	1.343
r_angle_other_deg	0.914
r_mcbond_it	0.772

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.953
r_dihedral_angle_4_deg	17.982
r_dihedral_angle_3_deg	12.739
r_dihedral_angle_1_deg	6.935
r_scangle_it	3.585
r_scbond_it	2.275
r_angle_refined_deg	1.461
r_mcangle_it	1.343
r_angle_other_deg	0.914
r_mcbond_it	0.772
r_mcbond_other	0.259
r_chiral_restr	0.098
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11532
Nucleic Acid Atoms
Solvent Atoms	1254
Heterogen Atoms	130

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.