Experiment: 5EZW

Thiosulfate bound rat cysteine dioxygenase Y157H variant

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4KWJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	291	Hanging drops of 3 microL of approximately 25 mg/mL Y157H-CDO (20mM Tris-HCl, pH 8.0) and 1 microL reservoir buffer containing seeds from WT-CDO were allowed to equilibrate above the reservoir buffer (26% (w/v) polyethylene glycol 4000, 200 mM ammonium acetate, 100 mM sodium citrate).

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.75	α = 90
b = 57.75	β = 90
c = 122.42	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	93	IMAGE PLATE	RIGAKU RAXIS IV++	Osmic VariMax optics	2014-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.65	26.12	95.7	0.073	0.015	1	29.7	24.1		24590			20.18

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	68.3		0.823	0.247	0.815	2.4	11.7	853

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4KWJ	1.65	26.115	1.34	24543	2293	95.63	0.1726	0.1715	0.1759	0.1922	0.198	25.7695

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.765
f_angle_d	0.858
f_chiral_restr	0.053
f_bond_d	0.009
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1517
Nucleic Acid Atoms
Solvent Atoms	243
Heterogen Atoms	6

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction