6HRV | pdb_00006hrv

Crystal structure of the zebrafish peroxisomal SCP2-thiolase (type-1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZBG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.4	295	100 mM HEPES, pH 6.4, 18% PEG3350, 250 mM sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.3	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.16	α = 90
b = 81.94	β = 125.81
c = 96.81	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-F		2013-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	1.95	29.64	98.4	0.05	0.03	0.99	15.7	3.4		60799		3	34.8

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	1.95	2.05	99.3		0.42	0.22	0.87	2.94	3.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3ZBG	1.95	29.64	57744	3040	98.73	0.17131	0.16943	0.18	0.20702	0.21	RANDOM	34.182

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		0.97	0.22		-0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.815
r_dihedral_angle_3_deg	13.749
r_dihedral_angle_4_deg	12.675
r_dihedral_angle_1_deg	6.088
r_long_range_B_refined	5.212
r_long_range_B_other	5.212
r_scangle_it	4.301
r_scangle_other	4.3
r_scbond_it	2.822
r_scbond_other	2.822
r_mcangle_it	2.801
r_mcangle_other	2.8
r_mcbond_other	2.032
r_mcbond_it	2.031
r_angle_refined_deg	1.498
r_angle_other_deg	0.95
r_nbd_refined	0.209
r_nbtor_refined	0.171
r_symmetry_hbond_refined	0.166
r_nbd_other	0.154
r_symmetry_vdw_other	0.15
r_xyhbond_nbd_refined	0.128
r_symmetry_vdw_refined	0.106
r_chiral_restr	0.08
r_nbtor_other	0.076
r_xyhbond_nbd_other	0.048
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5860
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	10

Software

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