2Q3L | pdb_00002q3l

CRYSTAL STRUCTURE OF AN UNCHARACTERIZED PROTEIN FROM DUF3478 FAMILY WITH A SPOIIAA-LIKE FOLD (SHEW_3102) FROM SHEWANELLA LOIHICA PV-4 AT 2.25 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.33	277	NANODROP, 0.2M Sodium chloride, 37.0% 2-methyl-2,4-pentanediol, 0.1M Tris-HCl pH 7.33, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.387	α = 90
b = 113.963	β = 90
c = 130.692	γ = 90

Symmetry
Space Group	C 2 2 21

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)	2007-05-14	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97926, 0.97895	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	2.25	28.653	99	0.067	0.067	17.89	7.2		14575			41.73

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	2.25	2.31	100		0.467	0.467	3.6	7	1060

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.25	28.653	14570	754	98.78	0.184	0.181	0.19	0.239	0.23	RANDOM	48.526

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]
3.53			0.8		-4.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.892
r_dihedral_angle_4_deg	13.08
r_dihedral_angle_3_deg	11.555
r_scangle_it	7.995
r_scbond_it	5.703
r_dihedral_angle_1_deg	4.09
r_mcangle_it	2.845
r_angle_refined_deg	1.756
r_mcbond_it	1.684
r_angle_other_deg	0.871
r_mcbond_other	0.605
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.194
r_symmetry_vdw_other	0.182
r_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.179
r_symmetry_hbond_refined	0.174
r_metal_ion_refined	0.168
r_nbd_other	0.158
r_chiral_restr	0.093
r_nbtor_other	0.09
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1937
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	76

Software

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