3RT9

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


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
2.6253.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.087α = 90
b = 122.087β = 90
c = 155.509γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rMIRRORS2009-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97918APS19-BM

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
11.955099.60.0690.06931.757.94289342640-327.5
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)
11.951.9898.70.8480.8482.2476.7

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 2AX31.9525042640215099.420.1580.1570.192RANDOM35.091
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]
-0.25-0.250.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.468
r_dihedral_angle_4_deg14.848
r_dihedral_angle_3_deg13.827
r_dihedral_angle_1_deg5.881
r_scangle_it5.606
r_angle_other_deg4.204
r_scbond_it3.295
r_mcangle_it1.921
r_angle_refined_deg1.827
r_mcbond_it1.041
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.468
r_dihedral_angle_4_deg14.848
r_dihedral_angle_3_deg13.827
r_dihedral_angle_1_deg5.881
r_scangle_it5.606
r_angle_other_deg4.204
r_scbond_it3.295
r_mcangle_it1.921
r_angle_refined_deg1.827
r_mcbond_it1.041
r_chiral_restr0.11
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_gen_planes_other0.008
r_bond_other_d
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3773
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms155

Software

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