2PBL

Crystal structure of a putative thioesterase (tm1040_2492) from silicibacter sp. tm1040 at 1.79 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	NANODROP, 0.2M MgCl2, 30.0% PEG 4000, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.197	α = 90
b = 74.438	β = 113.39
c = 95.727	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-03-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97937, 0.91837, 0.97910	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.79	29.45	99.9	0.108	0.108	4.8	3.2		93727			18.53

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.84	100		0.653	0.653	1.1	3.1	6901

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.79	29.45	93699	4700	99.86	0.224	0.224	0.221	0.27	RANDOM	17.196

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]
0.35		-0.33	-1.4		0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.609
r_dihedral_angle_4_deg	16.333
r_dihedral_angle_3_deg	10.28
r_scangle_it	6.855
r_scbond_it	5.298
r_dihedral_angle_1_deg	4.279
r_mcangle_it	2.793
r_mcbond_it	1.997
r_angle_refined_deg	1.71
r_angle_other_deg	1.014
r_mcbond_other	0.789
r_symmetry_hbond_refined	0.257
r_symmetry_vdw_other	0.241
r_xyhbond_nbd_refined	0.229
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.203
r_nbtor_refined	0.18
r_nbd_other	0.176
r_metal_ion_refined	0.156
r_chiral_restr	0.1
r_nbtor_other	0.088
r_xyhbond_nbd_other	0.031
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8049
Nucleic Acid Atoms
Solvent Atoms	1310
Heterogen Atoms	51

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing