3RS9

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 P1,P3-Di(adenosine-5') triphosphate


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
2.6253

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.073α = 90
b = 122.073β = 90
c = 155.292γ = 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
12.15099.60.0770.07734.075113434934168-332.9
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)
12.12.1496.10.7950.7952.1435.7

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 2AX32.1035034168172799.490.1590.1580.193RANDOM38.434
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]
-0.42-0.420.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.354
r_dihedral_angle_4_deg16.953
r_dihedral_angle_3_deg14.685
r_dihedral_angle_1_deg6.02
r_scangle_it4.807
r_angle_other_deg4.203
r_scbond_it2.973
r_angle_refined_deg1.747
r_mcangle_it1.643
r_mcbond_it0.881
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.354
r_dihedral_angle_4_deg16.953
r_dihedral_angle_3_deg14.685
r_dihedral_angle_1_deg6.02
r_scangle_it4.807
r_angle_other_deg4.203
r_scbond_it2.973
r_angle_refined_deg1.747
r_mcangle_it1.643
r_mcbond_it0.881
r_chiral_restr0.107
r_bond_refined_d0.02
r_gen_planes_other0.008
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 Atoms132
Heterogen Atoms66

Software

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