1O7G

NAPHTHALENE 1,2-DIOXYGENASE WITH NAPHTHALENE BOUND IN THE ACTIVE SITE.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EG9	PDB ENTRY 1EG9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		AMMONIUM SULPHATE 2M, MES 0.1M, DIOXANE 2-3%, pH 6.00

Crystal Properties
Matthews coefficient	Solvent content
2.56	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.67	α = 90
b = 139.67	β = 90
c = 208.109	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	CCD	ADSC CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	1.7	20	95.9	0.059	11.3	5.49		82025

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	1.7	1.73	97.5		0.19

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-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1EG9	1.7	25	77908	4117	95.9	0.163	0.187	RANDOM	19.98

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]
0.53	0.27		0.53		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.971
r_dihedral_angle_1_deg	5.361
r_scangle_it	4.773
r_scbond_it	2.977
r_mcangle_it	1.982
r_angle_refined_deg	1.811
r_symmetry_vdw_refined	1.166
r_mcbond_it	1.103
r_angle_other_deg	0.847
r_symmetry_hbond_refined	0.606
r_xyhbond_nbd_other	0.277
r_nbd_refined	0.253
r_xyhbond_nbd_refined	0.248
r_nbtor_other	0.229
r_symmetry_vdw_other	0.213
r_nbd_other	0.21
r_chiral_restr	0.118
r_bond_refined_d	0.019
r_metal_ion_refined	0.01
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5089
Nucleic Acid Atoms
Solvent Atoms	519
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling