1W3N

Sulfolobus solfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with D-KDG


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% PEG4000, 8% ISOPROPANOL, pH 6.00
Crystal Properties
Matthews coefficientSolvent content
2.754.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.797α = 90
b = 131.269β = 90
c = 132.759γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-10-03MSINGLE 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
12.139.2970.087.3683235522.03
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)
12.12.21970.312.55.9

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 1W372.14074888834796.80.1570.1510.213RANDOM23.06
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]
-1.1361.633-0.497
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.683
r_scangle_it5.595
r_scbond_it3.455
r_mcangle_it1.922
r_angle_refined_deg1.874
r_mcbond_it1.106
r_nbtor_refined0.317
r_nbd_refined0.216
r_symmetry_vdw_refined0.191
r_symmetry_hbond_refined0.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.683
r_scangle_it5.595
r_scbond_it3.455
r_mcangle_it1.922
r_angle_refined_deg1.874
r_mcbond_it1.106
r_nbtor_refined0.317
r_nbd_refined0.216
r_symmetry_vdw_refined0.191
r_symmetry_hbond_refined0.183
r_xyhbond_nbd_refined0.172
r_chiral_restr0.135
r_bond_refined_d0.025
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 Atoms812
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing