3RTD

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 NADH and ADP.


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
2.652.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.81α = 90
b = 121.81β = 90
c = 155.221γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBERYLLIUM LENSES2010-03-19MSINGLE 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
12.35098.70.0670.06723.4615.92631525944-342.4
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)
12.32.34980.7510.7511.8325.1

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 2AX32.35025932132298.650.1670.1640.219RANDOM44.989
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]
-0.18-0.180.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.504
r_dihedral_angle_4_deg17.123
r_dihedral_angle_3_deg16.547
r_dihedral_angle_1_deg6.308
r_scangle_it4.69
r_angle_other_deg4.169
r_scbond_it2.906
r_angle_refined_deg1.882
r_mcangle_it1.728
r_mcbond_it0.914
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.504
r_dihedral_angle_4_deg17.123
r_dihedral_angle_3_deg16.547
r_dihedral_angle_1_deg6.308
r_scangle_it4.69
r_angle_other_deg4.169
r_scbond_it2.906
r_angle_refined_deg1.882
r_mcangle_it1.728
r_mcbond_it0.914
r_chiral_restr0.102
r_bond_refined_d0.021
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 Atoms3778
Nucleic Acid Atoms
Solvent Atoms70
Heterogen Atoms110

Software

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