6HSJ

Crystal structure of the zebrafish peroxisomal SCP2-thiolase (type-1) in complex with CoA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6HRV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	100 mM HEPES, pH 7.0, 15 % PEG3350, 250 mM sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.3	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.96	α = 90
b = 80.88	β = 126.29
c = 96.47	γ = 90

Symmetry
Space Group	C 1 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	PIXEL	DECTRIS PILATUS 2M		2015-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9174	Diamond	I04-1

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	1.46	47.59	98.2	0.11	0.04	0.998	13.7	7.5		140415		2.9	18.4

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	1.46	1.56	98.2		0.68	0.19	0.856	2.85	7.5

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	6HRV	1.46	47.59	133408	7005	98.46	0.15736	0.15648	0.17423	RANDOM	14.128

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]
-0.2		0.35	-0.25		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.563
r_dihedral_angle_3_deg	12.462
r_dihedral_angle_4_deg	11.699
r_dihedral_angle_1_deg	6.421
r_long_range_B_other	4.43
r_long_range_B_refined	4.429
r_scangle_it	3.236
r_scangle_other	3.236
r_scbond_it	2.067
r_scbond_other	2.067
r_mcangle_it	1.805
r_mcangle_other	1.805
r_angle_refined_deg	1.589
r_angle_other_deg	1.52
r_mcbond_it	1.154
r_mcbond_other	1.153
r_nbd_refined	0.222
r_nbd_other	0.178
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.159
r_symmetry_vdw_refined	0.156
r_symmetry_vdw_other	0.153
r_symmetry_hbond_refined	0.116
r_nbtor_other	0.083
r_chiral_restr	0.078
r_xyhbond_nbd_other	0.012
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5872
Nucleic Acid Atoms
Solvent Atoms	542
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing