4KWK

Rat cysteine dioxygenase with cysteine persulfide bound to active site iron

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ELN	PDB entry 3eln

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	297	Hanging drops of 1.5 microL of approximately 8 mg/mL CDO and 1.5 microL reservoir buffer were allowed to equilibrate above the reservoir buffer (24-34% (w/v) polyethylene glycol 4000, 100-250 mM ammonium acetate, 100 mM sodium citrate, 0-4 mM dithionite, 40 mM L-cysteine). Crystals grew as needles or starbursts of approximately 0.1 mm in length in one week, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.75	α = 90
b = 57.75	β = 90
c = 122.67	γ = 90

Symmetry
Space Group	P 43 21 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 210r	Double Si with sagittaly bent second crystal	2012-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.95370	Australian Synchrotron	MX1

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	1.95	52.25	99.9	0.042	67.5	16.1	15914	15914		1.75	19.2

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	1.95	2.05	99.8		0.213	17.5	16.9	2257

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3eln	1.95	33.99	15876	15053	807	99.77	0.19288	0.19137	0.22194	The same R-free flags as PDB 3eln	21.459

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]
-0.19			-0.19		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.74
r_dihedral_angle_3_deg	13.967
r_dihedral_angle_4_deg	12.413
r_dihedral_angle_1_deg	5.835
r_angle_refined_deg	1.377
r_chiral_restr	0.103
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1519
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	9

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling