3CE8 | pdb_00003ce8

Crystal structure of a duf3240 family protein (sbal_0098) from shewanella baltica os155 at 2.40 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	NANODROP, 0.727M Ammonium dihydrogen phosphate, 0.114M Ammonium dihydrogen phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.285	α = 90
b = 71.285	β = 90
c = 71.285	γ = 90

Symmetry
Space Group	P 21 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2008-02-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97926, 0.97879	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	2.4	29.099	99.9	0.065	0.065	6.3	7.2		4934			68.285

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	2.4	2.46	100		0.619	0.619	1.2	7.4	364

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	2.4	29.099	4920	230	99.82	0.198	0.196	0.2	0.236	0.23	RANDOM	23.205

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.897
r_dihedral_angle_4_deg	15.18
r_dihedral_angle_3_deg	14.933
r_scangle_it	6.496
r_scbond_it	4.436
r_dihedral_angle_1_deg	3.832
r_mcangle_it	2.641
r_angle_refined_deg	1.765
r_angle_other_deg	1.582
r_mcbond_it	1.235

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.897
r_dihedral_angle_4_deg	15.18
r_dihedral_angle_3_deg	14.933
r_scangle_it	6.496
r_scbond_it	4.436
r_dihedral_angle_1_deg	3.832
r_mcangle_it	2.641
r_angle_refined_deg	1.765
r_angle_other_deg	1.582
r_mcbond_it	1.235
r_mcbond_other	0.164
r_chiral_restr	0.085
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	710
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	18

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
SHARP	phasing
SHELXD	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.