2HMJ | pdb_00002hmj

Crystal Structure of the Naphthalene 1,2-Dioxygenase Phe-352-Val Mutant.

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, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.894	α = 90
b = 139.894	β = 90
c = 208.58	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	1.5	15.99	99.2	0.078	9.6	4.38	123779	123779

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	1.5	1.55	94.4		0.518	2	2.88	11687

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	1.5	15.99	123709	123709	6218	99.08	0.157	0.157	0.155	0.17	0.186	0.2	RANDOM	15.965

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]
0.23	0.12		0.23		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.265
r_dihedral_angle_4_deg	16.569
r_dihedral_angle_3_deg	12.849
r_sphericity_free	9.078
r_dihedral_angle_1_deg	6.477
r_scangle_it	3.515
r_scbond_it	2.567
r_sphericity_bonded	2.28
r_rigid_bond_restr	1.859
r_mcangle_it	1.559
r_angle_refined_deg	1.418
r_mcbond_it	1.334
r_angle_other_deg	0.891
r_mcbond_other	0.397
r_symmetry_vdw_other	0.244
r_nbd_refined	0.21
r_nbd_other	0.206
r_nbtor_refined	0.18
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.153
r_symmetry_vdw_refined	0.151
r_chiral_restr	0.088
r_nbtor_other	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_metal_ion_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5069
Nucleic Acid Atoms
Solvent Atoms	754
Heterogen Atoms	89

Software

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