3BU7

Crystal Structure and Biochemical Characterization of GDOsp, a Gentisate 1,2-Dioxygenase from Silicibacter Pomeroyi

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D40	PDB ENTRY 2D40

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop		289	PEG3350,NaI, hanging drop, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.999	α = 90
b = 129.999	β = 90
c = 246.255	γ = 120

Symmetry
Space Group	H 3 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	IMAGE PLATE	RIGAKU RAXIS IV++			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	2.8	50	99.9	0.112	8.2	11.2		20056

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)
	2.8	2.9	100		0.423		11.3	1989

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2D40	2.8	41.93	20042	1019	99.8	0.212	0.21	0.245	RANDOM	34.718

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]
0.48	0.24		0.48		-0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.601
r_dihedral_angle_3_deg	16.581
r_dihedral_angle_4_deg	13.256
r_dihedral_angle_1_deg	5.323
r_mcangle_it	1.474
r_scangle_it	0.991
r_angle_refined_deg	0.979
r_mcbond_it	0.852
r_scbond_it	0.634
r_nbtor_refined	0.296

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.601
r_dihedral_angle_3_deg	16.581
r_dihedral_angle_4_deg	13.256
r_dihedral_angle_1_deg	5.323
r_mcangle_it	1.474
r_scangle_it	0.991
r_angle_refined_deg	0.979
r_mcbond_it	0.852
r_scbond_it	0.634
r_nbtor_refined	0.296
r_nbd_refined	0.185
r_symmetry_vdw_refined	0.147
r_xyhbond_nbd_refined	0.11
r_symmetry_hbond_refined	0.108
r_chiral_restr	0.073
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5672
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction

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 R01GM133198.