1O5J

Crystal structure of Periplasmic divalent cation tolerance protein (TM1056) from Thermotoga maritima at 1.95 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	10.5	293	30% PEG-400, 0.1M CAPS pH 10.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.514	α = 90
b = 52.514	β = 90
c = 34.707	γ = 120

Symmetry
Space Group	P 3

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	APS	water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror	2002-10-25	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97944, 0.97924, 0.95658	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.95	45.48	100	0.068	32.91	7.49		7337			41.58

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.02	70.02		0.245	3.7	3.99	563

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	MAD	THROUGHOUT	1.95	45.48	6993	339	93.94	0.15907	0.15603	0.22061	RANDOM	39.27

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]
-2.39	-1.2		-2.39		3.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.307
r_dihedral_angle_4_deg	23.559
r_dihedral_angle_3_deg	16.609
r_scangle_it	7.133
r_dihedral_angle_1_deg	6.361
r_scbond_it	5.692
r_mcangle_it	3.116
r_mcbond_it	2.511
r_angle_refined_deg	1.441
r_angle_other_deg	0.804
r_xyhbond_nbd_refined	0.239
r_symmetry_hbond_refined	0.232
r_symmetry_vdw_other	0.214
r_nbd_refined	0.206
r_nbd_other	0.193
r_symmetry_vdw_refined	0.148
r_chiral_restr	0.097
r_nbtor_other	0.089
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	890
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
RESOLVE	phasing