3RS8

Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima in complex with ADP-ribose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AX3PDB ENTRY 2AX3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1M Na Cacodylate, 1.6 M Na Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6453.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.393α = 90
b = 122.393β = 90
c = 155.71γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBERYLLIUM LENSES2009-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.1501000.0840.08424.6328.23496734867-328.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.141000.8370.8372.2476.9

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 2AX32.15034734173999.850.1620.160.199RANDOM35.351
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]
-0.23-0.230.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.564
r_dihedral_angle_3_deg14.984
r_dihedral_angle_4_deg14.468
r_dihedral_angle_1_deg6.08
r_scangle_it4.812
r_angle_other_deg4.182
r_scbond_it2.91
r_angle_refined_deg1.856
r_mcangle_it1.678
r_mcbond_it0.923
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.564
r_dihedral_angle_3_deg14.984
r_dihedral_angle_4_deg14.468
r_dihedral_angle_1_deg6.08
r_scangle_it4.812
r_angle_other_deg4.182
r_scbond_it2.91
r_angle_refined_deg1.856
r_mcangle_it1.678
r_mcbond_it0.923
r_chiral_restr0.107
r_bond_refined_d0.02
r_gen_planes_other0.009
r_gen_planes_refined0.007
r_bond_other_d
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3777
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing