3I0Z

Crystal structure of putative putative tagatose-6-phosphate ketose/aldose isomerase (NP_344614.1) from STREPTOCOCCUS PNEUMONIAE TIGR4 at 1.70 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.1860M calcium acetate, 22.2000% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3246.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.635α = 90
b = 111.267β = 97.09
c = 126.6γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2009-01-17MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91837,0.97964SSRLBL9-2

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
11.729.748990.0820.0827.2252.88586416.104
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)
11.71.74980.5320.5321.42.86303

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 DIFFRACTIONMADTHROUGHOUT1.729.74885861430298.870.1410.1390.178RANDOM20.225
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]
-0.810.130.460.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.411
r_dihedral_angle_4_deg16.541
r_dihedral_angle_3_deg11.772
r_dihedral_angle_1_deg5.84
r_scangle_it5.585
r_scbond_it4.373
r_mcangle_it2.496
r_mcbond_it1.982
r_angle_refined_deg1.521
r_angle_other_deg0.863
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.411
r_dihedral_angle_4_deg16.541
r_dihedral_angle_3_deg11.772
r_dihedral_angle_1_deg5.84
r_scangle_it5.585
r_scbond_it4.373
r_mcangle_it2.496
r_mcbond_it1.982
r_angle_refined_deg1.521
r_angle_other_deg0.863
r_mcbond_other0.572
r_symmetry_vdw_refined0.442
r_symmetry_vdw_other0.422
r_symmetry_hbond_refined0.292
r_nbd_refined0.222
r_xyhbond_nbd_refined0.207
r_nbd_other0.2
r_nbtor_refined0.187
r_chiral_restr0.097
r_nbtor_other0.091
r_bond_refined_d0.017
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 Atoms6021
Nucleic Acid Atoms
Solvent Atoms825
Heterogen Atoms67

Software

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