3L2H

Crystal structure of Putative sugar phosphate isomerase (AFE_0303) from Acidithiobacillus ferrooxidans ATCC 23270 at 1.85 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP10.52770.2000M sodium chloride, 20.0000% polyethylene glycol 8000, 0.1M CAPS pH 10.5, 0.001 M alpha-ketoglutaric acid, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.3463.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.876α = 90
b = 93.744β = 90
c = 139.042γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2009-07-08MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837,0.97925,0.97876SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.8529.48896.30.06210.1184481-324.678
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9295.30.7291.4

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 DIFFRACTIONMADTHROUGHOUT1.8529.488844284216990.1810.180.21RANDOM21.563
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]
0.540.87-1.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.933
r_dihedral_angle_4_deg14.784
r_dihedral_angle_3_deg12.93
r_dihedral_angle_1_deg5.75
r_angle_refined_deg1.707
r_scangle_it1.694
r_mcangle_it1.587
r_scbond_it1.087
r_mcbond_it0.939
r_angle_other_deg0.844
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.933
r_dihedral_angle_4_deg14.784
r_dihedral_angle_3_deg12.93
r_dihedral_angle_1_deg5.75
r_angle_refined_deg1.707
r_scangle_it1.694
r_mcangle_it1.587
r_scbond_it1.087
r_mcbond_it0.939
r_angle_other_deg0.844
r_mcbond_other0.21
r_chiral_restr0.07
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4965
Nucleic Acid Atoms
Solvent Atoms732
Heterogen Atoms115

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing