2CDA

Sulfolobus solfataricus Glucose Dehydrogenase 1 in complex with NADP


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 MM TRIS (PH 8.0), 4.5 % PROPAN-2-OL
Crystal Properties
Matthews coefficientSolvent content
2.757.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.62α = 90
b = 92.296β = 90
c = 138.264γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-06-12MSINGLE 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
12.2851.298.80.1112.85.238690
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)
12.282.499.60.266.35.2

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 2CD92.28138.6838076200898.10.1980.1960.246RANDOM20.24
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]
-0.161.6-1.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.148
r_dihedral_angle_4_deg20.855
r_dihedral_angle_3_deg16.962
r_dihedral_angle_1_deg7.531
r_scangle_it3.782
r_scbond_it2.512
r_angle_refined_deg1.817
r_mcangle_it1.688
r_mcbond_it1.034
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.148
r_dihedral_angle_4_deg20.855
r_dihedral_angle_3_deg16.962
r_dihedral_angle_1_deg7.531
r_scangle_it3.782
r_scbond_it2.512
r_angle_refined_deg1.817
r_mcangle_it1.688
r_mcbond_it1.034
r_nbtor_refined0.309
r_symmetry_hbond_refined0.219
r_nbd_refined0.212
r_symmetry_vdw_refined0.201
r_xyhbond_nbd_refined0.155
r_chiral_restr0.123
r_bond_refined_d0.019
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 Atoms5657
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
AMoREphasing