3E57

Crystal structure of Tm1382, a putative Nudix hydrolase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	0.1 M Trisodium Citrate pH 5.5, PEG 3000, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.589	α = 90
b = 62.879	β = 98.37
c = 73.896	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 225 mm CCD		2008-04-01	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	ADSC QUANTUM 315		2008-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	0.97933	APS	22-BM
2	SYNCHROTRON	ALS BEAMLINE 5.0.2	1	ALS	5.0.2

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	1.89	50	99.9	0.059		3.7		34267

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.9	1.97	100		0.387		3.7	3396

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.89	40	34212	1714	99.23	0.201	0.199	0.24	RANDOM	32.51

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]
-0.68		-0.17	-0.15		0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.955
r_dihedral_angle_3_deg	15.02
r_dihedral_angle_4_deg	13.211
r_dihedral_angle_1_deg	5.907
r_scangle_it	2.863
r_scbond_it	2.08
r_mcangle_it	1.342
r_mcbond_it	1.247
r_angle_refined_deg	1.216
r_angle_other_deg	0.798
r_symmetry_hbond_refined	0.235
r_symmetry_vdw_other	0.192
r_nbd_other	0.188
r_nbd_refined	0.187
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.173
r_symmetry_vdw_refined	0.169
r_mcbond_other	0.163
r_nbtor_other	0.085
r_chiral_restr	0.072
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2972
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling