2H6E | pdb_00002h6e

Crystal structure of the D-arabinose dehydrogenase from Sulfolobus solfataricus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.552934 mg/ml protein, 0.1 M HEPES-NaOH, 10% v/v Jeffamine-600, pH 8.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.346.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.019α = 90
b = 84.019β = 90
c = 194.979γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHmirrors2005-01-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.21.2827BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.85099.112.43252532525
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.86937

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.8423078130781164298.870.196740.196740.19490.20.232160.24RANDOM21.344
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]
0.870.87-1.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.739
r_dihedral_angle_4_deg13.943
r_dihedral_angle_3_deg13.56
r_dihedral_angle_1_deg9.777
r_scangle_it5.895
r_scbond_it4.509
r_mcangle_it2.51
r_mcbond_it1.935
r_angle_refined_deg1.285
r_angle_other_deg0.903
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.739
r_dihedral_angle_4_deg13.943
r_dihedral_angle_3_deg13.56
r_dihedral_angle_1_deg9.777
r_scangle_it5.895
r_scbond_it4.509
r_mcangle_it2.51
r_mcbond_it1.935
r_angle_refined_deg1.285
r_angle_other_deg0.903
r_mcbond_other0.548
r_symmetry_vdw_other0.245
r_nbd_refined0.199
r_nbd_other0.185
r_xyhbond_nbd_refined0.182
r_metal_ion_refined0.182
r_symmetry_hbond_refined0.173
r_nbtor_refined0.17
r_symmetry_vdw_refined0.143
r_nbtor_other0.084
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2412
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms2

Software

Software
Software NamePurpose
MAR345dtbdata collection
HKL-2000data reduction
SOLVEphasing
REFMACrefinement
HKL-2000data scaling