1W3T

Sulfolobus solfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with D-KDGal, D-Glyceraldehyde and pyruvate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W37PDB ENTRY 1W37

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
160.1M HEPES PH6, 13% PEG4,000, 8% ISOPROPANOL, pH 6.00
Crystal Properties
Matthews coefficientSolvent content
2.855.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.43α = 90
b = 131.733β = 90
c = 132.859γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.139.899.90.0877.885931521.16
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)
12.12.2199.90.223.37.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1W372.14077251867899.90.1550.150.204RANDOM21.08
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]
-0.7190.914-0.194
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.565
r_scangle_it5.687
r_scbond_it3.432
r_mcangle_it1.949
r_angle_refined_deg1.799
r_mcbond_it1.1
r_nbtor_refined0.317
r_nbd_refined0.219
r_xyhbond_nbd_refined0.17
r_symmetry_vdw_refined0.152
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.565
r_scangle_it5.687
r_scbond_it3.432
r_mcangle_it1.949
r_angle_refined_deg1.799
r_mcbond_it1.1
r_nbtor_refined0.317
r_nbd_refined0.219
r_xyhbond_nbd_refined0.17
r_symmetry_vdw_refined0.152
r_chiral_restr0.127
r_symmetry_hbond_refined0.111
r_bond_refined_d0.023
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9302
Nucleic Acid Atoms
Solvent Atoms819
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing