3VCA | pdb_00003vca

Quaternary Ammonium Oxidative Demethylation: X-ray Crystallographic, Resonance Raman and UV-visible Spectroscopic Analysis of a Rieske-type Demethylase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	100 mM HEPES buffer, 10 % PEG 3350, 10 % glycerol, 25 mM hexamine cobalt, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.667	α = 90
b = 97.667	β = 90
c = 179.325	γ = 120

Symmetry
Space Group	P 63 2 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	ADSC QUANTUM 210		2008-03-05	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210		2008-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	1.0	NSLS	X12C
2	SYNCHROTRON	NSLS BEAMLINE X12C	1.738	NSLS	X12C

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
1,2	1.59	28.191	99.9	0.08	40.78	16.3	68467	68467	2	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	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	SAD	1.59	28.191	65657	65657	6532	95.97	0.1752	0.1736	0.1681	0.1895	0.1836	Random, 10%	18.7

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]
0.379			0.379		-0.758

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.63
f_angle_d	1.18
f_chiral_restr	0.075
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3159
Nucleic Acid Atoms
Solvent Atoms	610
Heterogen Atoms	19

Software

Software
Software Name	Purpose
CBASS	data collection
SHELXS	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.