7REZ

MYCOBACTERIUM ABSCESSUS TRNA METHYLTRANSFERASE IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6NVR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293Protein at 24mg/ml was incubated with 10mM SAH in DMSO in a 1 to 1 ratio; Buffer 2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5. Drops were formed 1 to 1 ratio and crystals cryo protected by adding 1 microliter of 50 percent Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.6453.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.242α = 90
b = 79.094β = 90
c = 86.631γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-20.9794NSLS-II17-ID-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.6429.2299.610.69913.16313025.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.641.68195.50.87

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6NVR1.6429.211.3563047315399.640.1880.18650.2157RANDOM29.26
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.832
f_angle_d0.9744
f_chiral_restr0.0625
f_plane_restr0.0114
f_bond_d0.0064
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3293
Nucleic Acid Atoms
Solvent Atoms389
Heterogen Atoms52

Software

Software
Software NamePurpose
PHENIXrefinement
ADDREFdata reduction
XDSdata scaling
MOLREPphasing