2HKV | pdb_00002hkv

CRYSTAL STRUCTURE OF A PUTATIVE MEMBER OF THE DINB FAMILY (EXIG_1237) FROM EXIGUOBACTERIUM SIBIRICUM 255-15 AT 1.70 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP		277	20.0% PEG-3350, 0.2M MgSO4,, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2	VAPOR DIFFUSION,SITTING DROP,NANODROP		293	20.0% PEG-3350, 0.2M MgSO4,, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.02	α = 90
b = 45.02	β = 90
c = 131.18	γ = 120

Symmetry
Space Group	P 32 2 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 collimating mirror, toroid focusing mirror	2006-06-17	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2006-06-17	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97925	SSRL	BL9-2
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.92522, 0.97934	SSRL	BL9-2

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	1.7	25.094	99.8	0.115	9.58	9.38		17704			37.034

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	1.7	1.76	99.8		0.97	1.99	7.01	1533

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.7	25.094	17699	1361	99.86	0.185	0.18514	0.181	0.19	0.227	0.28	RANDOM	33.948

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]
-0.63	-0.32		-0.63		0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.465
r_dihedral_angle_4_deg	20.044
r_dihedral_angle_3_deg	14.219
r_scangle_it	7.64
r_scbond_it	5.706
r_dihedral_angle_1_deg	5.273
r_mcangle_it	3.507
r_mcbond_it	2.642
r_angle_refined_deg	1.451
r_angle_other_deg	1.025
r_mcbond_other	0.607
r_metal_ion_refined	0.401
r_symmetry_vdw_other	0.302
r_symmetry_vdw_refined	0.292
r_nbd_refined	0.223
r_nbtor_refined	0.191
r_nbd_other	0.179
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.1
r_symmetry_hbond_refined	0.092
r_nbtor_other	0.091
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1197
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	4

Software

Software
Software Name	Purpose
MolProbity	model building
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
SOLVE	phasing