2VC5

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	1DPM	PDB ENTRY 1DPM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		50MM TRIS-HCL PH 8, 15-18% PEG 8000, 0.1MM COCL2

Crystal Properties
Matthews coefficient	Solvent content
2.5	48.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.16	α = 90
b = 104.82	β = 90
c = 155.36	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	MARRESEARCH		2006-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A		ESRF	BM30A

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	2.59	44.9	95.3	0.16	11.69	3.6		85611		2

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	PDB ENTRY 1DPM	2.6	44.9	42121	2234	99.4	0.225	0.222	0.22	0.282	0.28	RANDOM	38.8

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]
0.87			-0.2		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.472
r_dihedral_angle_3_deg	18.412
r_dihedral_angle_4_deg	13.899
r_dihedral_angle_1_deg	5.856
r_angle_refined_deg	1.061
r_mcangle_it	0.423
r_scangle_it	0.409
r_nbtor_refined	0.301
r_scbond_it	0.249
r_mcbond_it	0.247
r_nbd_refined	0.19
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.168
r_symmetry_vdw_refined	0.164
r_symmetry_hbond_refined	0.053
r_bond_refined_d	0.007
r_gen_planes_refined	0.002
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	242
Heterogen Atoms	104

Software

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