Experiment: 3OBZ

Crystal structure of human phytanoyl-COA dioxygenase phyhd1 2-oxoglutarate and iron complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		In-house SAD structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	296	7%(v/v) PEG 3350, 0.2M calcium acetate and 0.2M KCl Crystals were grown in anaerobic environment and soaked with FeSO4 and 2-oxoglutarate to form complex, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.366	α = 90
b = 92.366	β = 90
c = 81.754	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	100	CCD	OXFORD TITAN CCD	multilayer	2007-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION SUPERNOVA	1.54

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	2.15	24.307	99.8	0.067	0.067	17.8	3.2	22253	22253

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.15	2.27	99.7		0.371	0.371	0.448	0.248	2	3.1	3181

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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	In-house SAD structure	2.15	24.307	22230	1081	99.7	0.2328	0.242	0.2744	0.2361	RANDOM	36.0944

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]
-2.258	-0.809		-2.258		4.516

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	3.225
c_mcangle_it	2.203
c_scbond_it	2.091
c_mcbond_it	1.326

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2278
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	11

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data collection
CrysalisPro	data reduction