2HMO | pdb_00002hmo

Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to 3-Nitrotoluene.

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
2.71	54.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.211	α = 90
b = 140.211	β = 90
c = 208.271	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	15.95	99.2	0.1	11.8	7.07	102411	102411

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	96.6		0.43	2.1	2.62	9895

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	RIGID BODY REFINEMENT	THROUGHOUT	1O7H	1.6	15.95	102382	102382	5122	99.07	0.162	0.162	0.161	0.18	0.197	0.21	RANDOM	17.437

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]
0.45	0.23		0.45		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.718
r_dihedral_angle_4_deg	17.552
r_dihedral_angle_3_deg	12.584
r_sphericity_free	8.304
r_dihedral_angle_1_deg	6.454
r_scangle_it	3.095
r_scbond_it	2.284
r_sphericity_bonded	1.953
r_rigid_bond_restr	1.648
r_angle_refined_deg	1.377
r_mcangle_it	1.369
r_mcbond_it	1.162
r_angle_other_deg	0.98
r_mcbond_other	0.333
r_symmetry_vdw_other	0.243
r_nbd_refined	0.209
r_nbd_other	0.204
r_symmetry_vdw_refined	0.188
r_nbtor_refined	0.179
r_metal_ion_refined	0.167
r_xyhbond_nbd_refined	0.15
r_symmetry_hbond_refined	0.121
r_chiral_restr	0.112
r_nbtor_other	0.086
r_bond_refined_d	0.011
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	5089
Nucleic Acid Atoms
Solvent Atoms	716
Heterogen Atoms	113

Software

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