2HMN

Crystal Structure of the Naphthalene 1,2-Dioxygenase F352V Mutant Bound to Anthracene.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O7H

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
2.68	54.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.457	α = 90
b = 139.457	β = 90
c = 208.219	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	1.7	16.91	99.7	0.072	11.1	5.55	85038	85038

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)
	1.7	1.76	100		0.481	2.9	5.47	8437

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	1.7	16.91	84962	84962	4248	99.52	0.161	0.161	0.159	0.194	RANDOM	19.986

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]
0.41	0.2		0.41		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.018
r_dihedral_angle_4_deg	17.952
r_dihedral_angle_3_deg	13.041
r_sphericity_free	8.274
r_dihedral_angle_1_deg	6.379
r_scangle_it	3.075
r_scbond_it	2.259
r_sphericity_bonded	2.185
r_rigid_bond_restr	1.714
r_mcangle_it	1.511
r_angle_refined_deg	1.381
r_mcbond_it	1.265
r_angle_other_deg	0.886
r_mcbond_other	0.385
r_symmetry_vdw_other	0.253
r_nbd_refined	0.209
r_nbd_other	0.206
r_symmetry_vdw_refined	0.187
r_nbtor_refined	0.18
r_symmetry_hbond_refined	0.174
r_xyhbond_nbd_refined	0.132
r_nbtor_other	0.087
r_chiral_restr	0.081
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	5079
Nucleic Acid Atoms
Solvent Atoms	581
Heterogen Atoms	116

Software

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