2CD9

Sulfolobus solfataricus Glucose Dehydrogenase 1 - apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherTHERMOPLASMA ACIDOPHILUM GDH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
112 % PEG, 0.1 M MES (PH 5.75), 3% (V/V) PROPAN-2-OL
Crystal Properties
Matthews coefficientSolvent content
2.753.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.501α = 90
b = 90.31β = 90
c = 138.941γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002004-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
11.838.196.70.0712.83.67391018.14
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)
11.81.992.90.2743.5

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 REPLACEMENTTHROUGHOUTTHERMOPLASMA ACIDOPHILUM GDH1.8141.4277521390596.20.1930.1910.23RANDOM20.62
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]
-0.0391.092-1.053
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.984
r_dihedral_angle_4_deg17.797
r_dihedral_angle_3_deg13.61
r_dihedral_angle_1_deg6.063
r_scangle_it3.695
r_scbond_it2.515
r_angle_refined_deg1.509
r_mcangle_it1.486
r_mcbond_it1.092
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.984
r_dihedral_angle_4_deg17.797
r_dihedral_angle_3_deg13.61
r_dihedral_angle_1_deg6.063
r_scangle_it3.695
r_scbond_it2.515
r_angle_refined_deg1.509
r_mcangle_it1.486
r_mcbond_it1.092
r_nbtor_refined0.307
r_nbd_refined0.204
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.159
r_symmetry_hbond_refined0.15
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.007
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 Atoms5693
Nucleic Acid Atoms
Solvent Atoms669
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing