2GUG

NAD-dependent formate dehydrogenase from Pseudomonas sp.101 in complex with formate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42930.8% PEG400, 2M Na formate, 0.1M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3347.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117α = 90
b = 54.98β = 95.74
c = 128.91γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2003-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8019EMBL/DESY, HamburgX13

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
12.2816.197.90.0497329044.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLREPTHROUGHOUTpdb entry 2NAC2.281007329069594369697.540.19970.195960.2692RANDOM36.737
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]
-3.560.014.58-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.671
r_dihedral_angle_4_deg18.227
r_dihedral_angle_3_deg17.353
r_dihedral_angle_1_deg7.363
r_scangle_it3.982
r_scbond_it2.729
r_angle_refined_deg1.862
r_mcangle_it1.769
r_mcbond_it1.052
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.671
r_dihedral_angle_4_deg18.227
r_dihedral_angle_3_deg17.353
r_dihedral_angle_1_deg7.363
r_scangle_it3.982
r_scbond_it2.729
r_angle_refined_deg1.862
r_mcangle_it1.769
r_mcbond_it1.052
r_nbtor_refined0.316
r_symmetry_vdw_refined0.305
r_symmetry_hbond_refined0.242
r_nbd_refined0.234
r_xyhbond_nbd_refined0.163
r_chiral_restr0.126
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_symmetry_vdw_other
r_nbd_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_angle_other_deg
r_mcbond_other
r_nbtor_other
r_gen_planes_other
r_bond_other_d
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11504
Nucleic Acid Atoms
Solvent Atoms389
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
MARHKLdata reduction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing