1VL8

Crystal structure of Gluconate 5-dehydrogenase (TM0441) from Thermotoga maritima at 2.07 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G6K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP4.2277Acetate pH 4.2, 35% Glycerol, 0.4M NH4H2PO3 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.8968.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.504α = 90
b = 123.504β = 90
c = 122.323γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAPSwater cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror2004-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BMAPS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.965089.420.08816.016.896122232.51
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.962.0372.830.6721.062.354917

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 REPLACEMENTTHROUGHOUT1g6k2.0743.6750440271591.50.151480.149990.17955RANDOM26.843
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]
-1.08-1.082.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.122
r_dihedral_angle_4_deg14.893
r_dihedral_angle_3_deg13.495
r_scangle_it6.908
r_dihedral_angle_1_deg5.97
r_scbond_it5.163
r_mcangle_it2.492
r_mcbond_it2.181
r_angle_refined_deg1.655
r_angle_other_deg0.947
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.122
r_dihedral_angle_4_deg14.893
r_dihedral_angle_3_deg13.495
r_scangle_it6.908
r_dihedral_angle_1_deg5.97
r_scbond_it5.163
r_mcangle_it2.492
r_mcbond_it2.181
r_angle_refined_deg1.655
r_angle_other_deg0.947
r_mcbond_other0.521
r_nbd_refined0.203
r_symmetry_vdw_other0.197
r_nbd_other0.176
r_nbtor_refined0.175
r_symmetry_hbond_refined0.159
r_symmetry_vdw_refined0.146
r_xyhbond_nbd_refined0.132
r_chiral_restr0.097
r_nbtor_other0.085
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3838
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms102

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement