3FJ1

Crystal structure of putative phosphosugar isomerase (YP_167080.1) from SILICIBACTER POMEROYI DSS-3 at 1.75 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.82770.2000M MgCl2, 20.0000% PEG-3350, No Buffer pH 5.8, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0239.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.4α = 90
b = 114.141β = 90
c = 197.279γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focusing mirrors in K-B geometry2008-10-12MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.94645,0.97967APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)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
11.7529.38698.10.1150.1150.1289.44.311767916.07
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.883.40.5960.5960.7071.22.77290

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 DIFFRACTIONMADTHROUGHOUT1.7529.386117606589797.90.1640.1620.195RANDOM14.586
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]
0.46-0.44-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.094
r_dihedral_angle_4_deg15.2
r_dihedral_angle_3_deg11.398
r_dihedral_angle_1_deg4.061
r_angle_refined_deg1.528
r_scangle_it1.306
r_mcangle_it1.164
r_angle_other_deg1.042
r_scbond_it0.868
r_mcbond_it0.752
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.094
r_dihedral_angle_4_deg15.2
r_dihedral_angle_3_deg11.398
r_dihedral_angle_1_deg4.061
r_angle_refined_deg1.528
r_scangle_it1.306
r_mcangle_it1.164
r_angle_other_deg1.042
r_scbond_it0.868
r_mcbond_it0.752
r_symmetry_vdw_other0.269
r_symmetry_hbond_refined0.238
r_nbd_refined0.218
r_mcbond_other0.205
r_nbd_other0.192
r_symmetry_vdw_refined0.192
r_xyhbond_nbd_refined0.187
r_nbtor_refined0.17
r_chiral_restr0.096
r_nbtor_other0.088
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9647
Nucleic Acid Atoms
Solvent Atoms1212
Heterogen Atoms15

Software

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