2RA9 | pdb_00002ra9

Crystal structure of a duf1285 family protein (sbal_2486) from shewanella baltica os155 at 1.40 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	277	NANODROP, 20.0% Isopropanol, 20.0% PEG 4000, 0.1M Citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.409	α = 90
b = 62.286	β = 90
c = 73.247	γ = 90

Symmetry
Space Group	P 21 21 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	ADSC QUANTUM 315		2007-08-30	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9795, 0.9798, 1.0000	ALS	8.2.2

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	1.4	29.854	99.6	0.058	0.058	7.8	4.9		35222		-4

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	1.4	1.44	98.5		0.613	0.613	1.3	4.6	2546

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	1.4	29.854	35168	1764	99.43	0.164	0.162	0.17	0.196	0.2	RANDOM	13.495

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]
-0.2			-0.1		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.717
r_dihedral_angle_3_deg	13.126
r_dihedral_angle_4_deg	10.076
r_dihedral_angle_1_deg	7.175
r_scangle_it	6.298
r_sphericity_free	5.761
r_scbond_it	4.634
r_sphericity_bonded	3.852
r_mcangle_it	3.445
r_rigid_bond_restr	2.629
r_mcbond_it	2.479
r_mcbond_other	1.528
r_angle_refined_deg	1.519
r_angle_other_deg	0.936
r_nbd_refined	0.24
r_nbd_other	0.21
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.179
r_symmetry_vdw_other	0.158
r_metal_ion_refined	0.115
r_symmetry_vdw_refined	0.113
r_symmetry_hbond_refined	0.112
r_chiral_restr	0.104
r_nbtor_other	0.083
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1018
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHARP	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SHELX	phasing