3RTG

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


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
2.6353.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.245α = 90
b = 122.245β = 90
c = 155.525γ = 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
12.055097.50.0790.07922.5247.23712536107-325.6
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)
12.052.0996.20.6340.6342.5436.2

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 2AX32.0525036106181197.270.1650.1630.196RANDOM31.735
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]
-0.44-0.440.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.447
r_dihedral_angle_4_deg17.812
r_dihedral_angle_3_deg14.525
r_dihedral_angle_1_deg6.121
r_scangle_it5.182
r_angle_other_deg4.18
r_scbond_it3.074
r_mcangle_it1.813
r_angle_refined_deg1.767
r_mcbond_it0.992
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.447
r_dihedral_angle_4_deg17.812
r_dihedral_angle_3_deg14.525
r_dihedral_angle_1_deg6.121
r_scangle_it5.182
r_angle_other_deg4.18
r_scbond_it3.074
r_mcangle_it1.813
r_angle_refined_deg1.767
r_mcbond_it0.992
r_chiral_restr0.101
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 Atoms3778
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms154

Software

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