6HSP

Crystal structure of the zebrafish peroxisomal SCP2-thiolase (type-1) in complex with CoA and octanoyl-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 MOPS, pH 7.0, 10 % PEG6000, 20% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.3	47.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.18	α = 90
b = 81.32	β = 126.08
c = 96.63	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 6M		2015-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	1.2822	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.73	42.88	99.1	0.09	0.06	0.996	8.42	3.2		85694		-3	28

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.73	1.83	97.6		0.63	0.38	0.403		2.6

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	MOLECULAR REPLACEMENT	THROUGHOUT	6HRV	1.73	42.88	81387	4301	99.38	0.19192	0.19006	0.22733	RANDOM	34.337

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]
0.61		0.24	0.75		-0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.086
r_dihedral_angle_4_deg	14.915
r_dihedral_angle_3_deg	13.048
r_long_range_B_refined	6.085
r_long_range_B_other	6.083
r_dihedral_angle_1_deg	5.954
r_scangle_it	4.808
r_scangle_other	4.808
r_scbond_it	3.192
r_scbond_other	3.191
r_mcangle_it	2.797
r_mcangle_other	2.797
r_mcbond_it	2.089
r_mcbond_other	2.084
r_angle_refined_deg	1.558
r_angle_other_deg	1.064
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.19
r_nbtor_refined	0.174
r_symmetry_vdw_other	0.159
r_nbd_other	0.154
r_xyhbond_nbd_refined	0.122
r_symmetry_vdw_refined	0.12
r_chiral_restr	0.096
r_nbtor_other	0.076
r_xyhbond_nbd_other	0.03
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5853
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	129

Software

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