2HMM

Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Anthracene

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	279.15	1.9-2.2 M Ammonium Sulfate, 4-6% Dioxane, 0.1 M MES, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.725	α = 90
b = 139.725	β = 90
c = 208.113	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	NOIR-1		2004-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.04021	ALS	4.2.2

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	1.6	15.97	98.5	0.069	10	3.16	100884	100884

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)
	1.6	1.66	95.5		0.449	2.3	2.94	9731

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	RIGID BODY REFINEMENT	THROUGHOUT	1O7H	1.6	15.97	100819	100819	5049	98.29	0.165	0.165	0.164	0.198	RANDOM	16.738

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		-0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.222
r_dihedral_angle_4_deg	18.333
r_dihedral_angle_3_deg	13.426
r_sphericity_free	9.64
r_dihedral_angle_1_deg	6.489
r_scangle_it	3.194
r_scbond_it	2.588
r_rigid_bond_restr	2.222
r_sphericity_bonded	2.143
r_mcangle_it	1.475
r_angle_refined_deg	1.422
r_mcbond_it	1.262
r_angle_other_deg	0.898
r_mcbond_other	0.333
r_symmetry_vdw_other	0.242
r_nbd_other	0.212
r_nbd_refined	0.211
r_symmetry_vdw_refined	0.191
r_nbtor_refined	0.181
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.144
r_nbtor_other	0.088
r_chiral_restr	0.083
r_metal_ion_refined	0.021
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5088
Nucleic Acid Atoms
Solvent Atoms	731
Heterogen Atoms	131

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction