2CDC

Sulfolobus solfataricus Glucose Dehydrogenase 1 in complex with NADP and Xylose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CD9PDB ENTRY 2CD9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18 % PEG 8000, 0.1 M TRIS (PH 8.0), 4.5 % (V/V) PROPAN-2-OL
Crystal Properties
Matthews coefficientSolvent content
2.2745.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.644α = 90
b = 91.032β = 89.98
c = 138.725γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.541.293.10.0512.42.1191673
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)
11.51.5880.10.282.51.9

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 2CD91.5138.6824050412721930.2060.2040.239RANDOM16.66
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]
-0.140.64-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.16
r_dihedral_angle_4_deg17.352
r_dihedral_angle_3_deg14.227
r_dihedral_angle_1_deg5.668
r_scangle_it2.402
r_scbond_it1.623
r_angle_refined_deg1.325
r_mcangle_it1.085
r_mcbond_it0.696
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.16
r_dihedral_angle_4_deg17.352
r_dihedral_angle_3_deg14.227
r_dihedral_angle_1_deg5.668
r_scangle_it2.402
r_scbond_it1.623
r_angle_refined_deg1.325
r_mcangle_it1.085
r_mcbond_it0.696
r_nbtor_refined0.308
r_nbd_refined0.217
r_symmetry_vdw_refined0.159
r_xyhbond_nbd_refined0.155
r_symmetry_hbond_refined0.134
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_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 Atoms11288
Nucleic Acid Atoms
Solvent Atoms1580
Heterogen Atoms312

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing