1VL1

Crystal structure of 6-phosphogluconolactonase (TM1154) from Thermotoga maritima at 1.70A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PBT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP2770.2M (NH4)2HCitrate, 20% PEG-3350 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.9335.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.733α = 90
b = 75.146β = 90
c = 148.443γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2004-04-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.555079.460.07516.593.862472923.98
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.6126.040.3252.932.57798

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1PBT1.5537.1123466126279.320.167170.165230.20395RANDOM22.367
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]
-0.312.44-2.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.484
r_dihedral_angle_4_deg16.694
r_dihedral_angle_3_deg11.733
r_dihedral_angle_1_deg6.249
r_scangle_it3.979
r_scbond_it2.733
r_angle_refined_deg1.62
r_mcangle_it1.535
r_mcbond_it1.151
r_angle_other_deg0.876
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.484
r_dihedral_angle_4_deg16.694
r_dihedral_angle_3_deg11.733
r_dihedral_angle_1_deg6.249
r_scangle_it3.979
r_scbond_it2.733
r_angle_refined_deg1.62
r_mcangle_it1.535
r_mcbond_it1.151
r_angle_other_deg0.876
r_symmetry_vdw_other0.364
r_mcbond_other0.327
r_symmetry_vdw_refined0.294
r_nbd_refined0.218
r_symmetry_hbond_refined0.194
r_nbd_other0.184
r_xyhbond_nbd_refined0.133
r_chiral_restr0.115
r_nbtor_other0.083
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1766
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms13

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement