3OJJ | pdb_00003ojj

Structure of Co-substituted Homoprotocatechuate 2,3-Dioxygenase from B.fuscum at 1.72 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, 0.1 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
2.43	49.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.539	α = 90
b = 152.075	β = 90
c = 96.491	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		2010-04-14	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315r		2010-03-21	M	SINGLE WAVELENGTH
3	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	DIAMOND BEAMLINE I03	0.9763	Diamond	I03
2	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	1.6050	SOLEIL	PROXIMA 1
3	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	1.6077	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	1.72	29.86	98.9	0.063	0.103	9	3.5	172043	170151		3	16.7

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)
	1.72	1.81	98.7		0.437	1.9	3.5	24631

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	1.72	29.62	161661	8442	98.64	0.14814	0.14664	0.17	0.17639	0.19	RANDOM	18.684

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		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.124
r_dihedral_angle_4_deg	18.473
r_dihedral_angle_3_deg	12.334
r_dihedral_angle_1_deg	7.15
r_scangle_it	3.06
r_scbond_it	2
r_angle_refined_deg	1.442
r_mcangle_it	1.116
r_angle_other_deg	0.915
r_mcbond_it	0.664

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.124
r_dihedral_angle_4_deg	18.473
r_dihedral_angle_3_deg	12.334
r_dihedral_angle_1_deg	7.15
r_scangle_it	3.06
r_scbond_it	2
r_angle_refined_deg	1.442
r_mcangle_it	1.116
r_angle_other_deg	0.915
r_mcbond_it	0.664
r_mcbond_other	0.225
r_chiral_restr	0.096
r_bond_refined_d	0.014
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	11523
Nucleic Acid Atoms
Solvent Atoms	1651
Heterogen Atoms	130

Software

Software
Software Name	Purpose
ADSC	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.