2RDB | pdb_00002rdb

X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2INC	PDB entry 2INC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	100 mM HEPES pH 7.5, 2.1-2.5 M Ammonium Sulfate, 2-4% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 182.42	α = 90
b = 182.42	β = 90
c = 67.962	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	101	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, double crystal monochromator, toroid focusing mirror	2006-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.979	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.1	50	85	0.059	0.064	19	6.1	75743	73939	2.1	2.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	83.3		0.307	0.541	19.4	6.2

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 (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 2INC	2.1	36.84	73882	60892	3226	84.67	0.22057	0.2172	0.22	0.2837	0.28	RANDOM	50.75

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]
-4.97	-2.49		-4.97		7.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.796
r_dihedral_angle_4_deg	23.779
r_dihedral_angle_3_deg	19.416
r_dihedral_angle_1_deg	9.269
r_scangle_it	5.257
r_scbond_it	4.141
r_angle_refined_deg	2.761
r_mcangle_it	2.452
r_mcbond_it	1.632
r_nbtor_refined	0.327
r_nbd_refined	0.256
r_symmetry_vdw_refined	0.218
r_chiral_restr	0.193
r_xyhbond_nbd_refined	0.187
r_symmetry_hbond_refined	0.133
r_bond_refined_d	0.034
r_gen_planes_refined	0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7341
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	46

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SSRL	data collection
HKL-2000	data reduction
HKL-2000	data scaling
EPMR	phasing