3BHN

Crystal structure of a dj-1/pfpi-like protein (shew_2856) from shewanella loihica pv-4 at 1.76 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	277	NANODROP, 0.2M Na Tartrate, 20.0% PEG 3350, No Buffer pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.32	α = 90
b = 71.32	β = 90
c = 180.63	γ = 120

Symmetry
Space Group	P 61 2 2

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	ADSC QUANTUM 315		2007-10-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9537, 0.9798, 0.9796	ALS	8.2.2

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	1.76	29.223	99.4	0.083	13.14	10.35		27863		-3	22.32

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	1.76	1.82	95.4		0.806	2

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	1.76	29.223	27782	1398	99.88	0.163	0.162	0.19	RANDOM	18.478

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]
0.59	0.3		0.59		-0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.769
r_dihedral_angle_4_deg	20.813
r_dihedral_angle_3_deg	12.681
r_scangle_it	6.046
r_dihedral_angle_1_deg	4.968
r_scbond_it	4.785
r_mcangle_it	2.502
r_mcbond_it	1.862
r_angle_refined_deg	1.397
r_angle_other_deg	0.984
r_mcbond_other	0.461
r_symmetry_hbond_refined	0.219
r_nbd_refined	0.213
r_nbd_other	0.192
r_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.174
r_symmetry_vdw_refined	0.169
r_symmetry_vdw_other	0.158
r_chiral_restr	0.092
r_nbtor_other	0.089
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1604
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction