2VC7

Structural basis for natural lactonase and promiscuous phosphotriesterase activities

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VC5	PDB ENTRY 2VC5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		TRIS-HCL 50MM PH 8, 15-18% W/V PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.5	40.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.383	α = 90
b = 104.124	β = 90
c = 153.051	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 CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.05	61.66	99.9	0.13	13.66	7.25		141906		2

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	2.05	2.15	92.8			7.1

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	PDB ENTRY 2VC5	2.05	61.66	82756	4370	99.9	0.239	0.237	0.287	RANDOM	28.86

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]
0.6			-0.17		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.315
r_dihedral_angle_3_deg	17.318
r_dihedral_angle_4_deg	16.479
r_dihedral_angle_1_deg	6.708
r_angle_refined_deg	1.119
r_scangle_it	0.438
r_mcangle_it	0.42
r_nbtor_refined	0.297
r_scbond_it	0.286
r_mcbond_it	0.257
r_nbd_refined	0.18
r_symmetry_vdw_refined	0.124
r_symmetry_hbond_refined	0.116
r_chiral_restr	0.104
r_xyhbond_nbd_refined	0.088
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10052
Nucleic Acid Atoms
Solvent Atoms	760
Heterogen Atoms	348

Software

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