5HXU | pdb_00005hxu

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

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BVQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	293	Protein at 15 mg/mL; reservoir was 2.5 M ammonium sulfate with 10% (v/v) MMT buffer at pH 9; sitting drop setup with 150 nL plus 150 nL drops; crystals cryo-protected with AP/E core 150 basestock (Mobile 1, Australia).

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.415	α = 90
b = 83.415	β = 90
c = 216.234	γ = 90

Symmetry
Space Group	P 41 21 2

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		2014-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	1.28221	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	1.83	45.7	98.1	22.2	26.6		67015

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	1.83	1.87	81		3.5	20.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4bvq	1.83	41.5	62328	3218	96.03	0.21268	0.21067	0.22	0.25165	0.26	RANDOM	25.162

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]
0.07			0.07		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.211
r_dihedral_angle_4_deg	18.184
r_dihedral_angle_3_deg	13.818
r_long_range_B_refined	7.198
r_long_range_B_other	7.105
r_scangle_other	6.082
r_dihedral_angle_1_deg	5.864
r_scbond_it	4.327
r_scbond_other	4.314
r_mcangle_it	3.967
r_mcangle_other	3.967
r_mcbond_it	3.109
r_mcbond_other	3.109
r_angle_refined_deg	1.729
r_angle_other_deg	1.594
r_chiral_restr	0.106
r_bond_refined_d	0.017
r_bond_other_d	0.01
r_gen_planes_refined	0.01
r_gen_planes_other	0.007
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	5432
Nucleic Acid Atoms
Solvent Atoms	617
Heterogen Atoms	45

Software

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