3RRB

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 AMP


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
2.6253.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.102α = 90
b = 122.102β = 90
c = 155.614γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMIRRORS2008-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.12712APS21-ID-D

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
12.45099.80.070.0738.5238.7200896200896-358.9
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)
12.42.4498.90.9380.9381.8145.7

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 2AX32.45023145119399.490.170.1670.216RANDOM58.275
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]
-0.83-0.831.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.863
r_dihedral_angle_4_deg16.037
r_dihedral_angle_3_deg15.562
r_dihedral_angle_1_deg6.329
r_scangle_it4.222
r_angle_other_deg4.22
r_scbond_it2.533
r_angle_refined_deg1.706
r_mcangle_it1.471
r_mcbond_it0.752
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.863
r_dihedral_angle_4_deg16.037
r_dihedral_angle_3_deg15.562
r_dihedral_angle_1_deg6.329
r_scangle_it4.222
r_angle_other_deg4.22
r_scbond_it2.533
r_angle_refined_deg1.706
r_mcangle_it1.471
r_mcbond_it0.752
r_chiral_restr0.096
r_bond_refined_d0.02
r_gen_planes_other0.007
r_gen_planes_refined0.006
r_bond_other_d
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3773
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms47

Software

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