3DFE

Crystal structure of a Putative Pii-Like Signaling Protein (YP_323533.1) from ANABAENA VARIABILIS ATCC 29413 at 2.35 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529335.0000% 2-propanol, 5.0000% PEG-1000, 35.0000% 2-propanol, 5.0000% PEG-1000, 0.1M Citrate pH 5.5, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2144.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.491α = 90
b = 78.749β = 100.56
c = 65.544γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2008-04-03MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837,0.97854SSRLBL11-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.3529.81499.90.0590.0597.93.82656057.051
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)
12.352.411000.6060.6061.33.81948

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 DIFFRACTIONMADTHROUGHOUT2.3529.81426543133999.930.2270.2240.267RANDOM48.862
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]
4.434.08-1.25-1.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.407
r_dihedral_angle_4_deg17.273
r_dihedral_angle_3_deg12.554
r_dihedral_angle_1_deg3.294
r_angle_refined_deg1.621
r_scangle_it1.248
r_mcangle_it1.089
r_angle_other_deg0.997
r_scbond_it0.981
r_mcbond_it0.734
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.407
r_dihedral_angle_4_deg17.273
r_dihedral_angle_3_deg12.554
r_dihedral_angle_1_deg3.294
r_angle_refined_deg1.621
r_scangle_it1.248
r_mcangle_it1.089
r_angle_other_deg0.997
r_scbond_it0.981
r_mcbond_it0.734
r_mcbond_other0.323
r_symmetry_vdw_refined0.277
r_nbd_refined0.203
r_nbd_other0.184
r_nbtor_refined0.18
r_symmetry_vdw_other0.161
r_xyhbond_nbd_refined0.127
r_chiral_restr0.099
r_nbtor_other0.087
r_bond_refined_d0.015
r_bond_other_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3582
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms8

Software

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