5HY4

Structure-function analysis of functionally diverse members of the cyclic amide hydrolase family of Toblerone fold enzymes

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5HY0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	281	Protein was concentrated to 4.2 mg/mL; reservoir was 20% PEG 3350 and 0.2 M magnesium acetate at 8 C; drops were 150 nL protein plus 150 nL reservoir.

Crystal Properties
Matthews coefficient	Solvent content
2.1	43.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.762	α = 90
b = 105.799	β = 90
c = 299.127	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315r		2014-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95370	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.56	46.7	99.5	12.5	7.5		95206

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.56	2.6	98.9		1.8	7.6

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	5HY0	2.56	46.7	90462	4666	99.38	0.2311	0.22943	0.26343	RANDOM	53.899

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]
-0.58			-1.37		1.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.808
r_dihedral_angle_4_deg	19.431
r_dihedral_angle_3_deg	14.658
r_long_range_B_other	11.375
r_long_range_B_refined	11.373
r_dihedral_angle_1_deg	7.244
r_mcangle_it	6.846
r_mcangle_other	6.846
r_scangle_other	6.243
r_mcbond_it	4.378
r_mcbond_other	4.377
r_scbond_it	3.923
r_scbond_other	3.923
r_angle_other_deg	2.097
r_angle_refined_deg	1.522
r_chiral_restr	0.081
r_bond_refined_d	0.013
r_bond_other_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.009
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19446
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms

Software

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