3SIY

Crystal structure of a DUF1989 family protein (TM1040_0329) from SILICIBACTER SP. TM1040 at 1.35 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	22.0% PEG 3350, 0.1M Magnesium Chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.907	α = 90
b = 48.132	β = 98.44
c = 144.732	γ = 90

Symmetry
Space Group	C 1 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 mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)	2010-02-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97971,0.97941	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	1.35	58.798	85.8	0.086	0.086	11.1	6.6	152479	152479			10.84

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	1.35	1.42	100		0.625	0.625	2.3	5.7	25878

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	1.35	58.798	152408	5488	85.65	0.1387	0.1373	0.1715	RANDOM	15.5987

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]
-0.19		0.33	0.54		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.025
r_dihedral_angle_4_deg	18.067
r_dihedral_angle_3_deg	12.039
r_dihedral_angle_1_deg	6.629
r_sphericity_free	6.605
r_scangle_it	4.02
r_sphericity_bonded	2.989
r_scbond_it	2.75
r_mcangle_it	1.976
r_angle_refined_deg	1.5
r_mcbond_it	1.302
r_rigid_bond_restr	1.217
r_angle_other_deg	0.924
r_mcbond_other	0.562
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7052
Nucleic Acid Atoms
Solvent Atoms	1086
Heterogen Atoms	13

Software

Software
Software Name	Purpose
XDS	data scaling
XSCALE	data scaling
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing
SHARP	phasing
SOLOMON	phasing
REFMAC	refinement
MolProbity	model building
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing