3GZI

CRYSTAL STRUCTURE OF a transcriptional regulator of the tetR family (SHEW_3567) FROM SHEWANELLA LOIHICA PV-4 AT 2.05 A RESOLUTION


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527740.0000% Ethylene-Glycol, 5.0000% PEG-3000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4249.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.83α = 90
b = 45.836β = 90
c = 68.694γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2009-01-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.0529.671000.0960.096104.81603234.881
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)RedundancyNumber Unique Reflections (All)
12.052.11000.7650.7651.84.91176

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.0529.671600479999.950.190.1870.248RANDOM38.319
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]
-0.01-0.720.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.787
r_dihedral_angle_4_deg18.422
r_dihedral_angle_3_deg14.828
r_scangle_it6.885
r_dihedral_angle_1_deg6.88
r_scbond_it5.407
r_mcangle_it3.238
r_mcbond_it2.373
r_angle_refined_deg1.477
r_angle_other_deg1.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.787
r_dihedral_angle_4_deg18.422
r_dihedral_angle_3_deg14.828
r_scangle_it6.885
r_dihedral_angle_1_deg6.88
r_scbond_it5.407
r_mcangle_it3.238
r_mcbond_it2.373
r_angle_refined_deg1.477
r_angle_other_deg1.101
r_mcbond_other0.467
r_symmetry_vdw_other0.281
r_nbd_refined0.238
r_nbd_other0.18
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.137
r_symmetry_hbond_refined0.13
r_symmetry_vdw_refined0.103
r_chiral_restr0.09
r_nbtor_other0.087
r_bond_refined_d0.016
r_xyhbond_nbd_other0.011
r_bond_other_d0.009
r_gen_planes_refined0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1595
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing