1O7M | pdb_00001o7m

NAPHTHALENE 1,2-DIOXYGENASE, BINARY COMPLEX WITH DIOXYGEN

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 = 140.277	α = 90
b = 140.277	β = 90
c = 208.754	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 MSC	CONFOCAL MIRRORS	2001-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R

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	1.75	30	94	0.063	10.2	3.67		80092

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	1.75	1.79	86.5		0.321	2.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1EG9	1.75	30	77729	771	98.9	0.178	0.19	0.187	0.2	RANDOM	14.3

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]
0.15	0.07		0.15		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.127
r_dihedral_angle_1_deg	5.045
r_scangle_it	3.62
r_scbond_it	2.263
r_angle_refined_deg	1.625
r_mcangle_it	1.514
r_angle_other_deg	1.228
r_mcbond_it	0.814
r_nbtor_other	0.33
r_symmetry_hbond_refined	0.304
r_nbd_refined	0.239
r_symmetry_vdw_other	0.22
r_nbd_other	0.217
r_xyhbond_nbd_refined	0.188
r_symmetry_vdw_refined	0.188
r_xyhbond_nbd_other	0.12
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_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	553
Heterogen Atoms	46

Software

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