3QUV

Crystal structure of a tRNA-guanine-N1-methyltransferase from Mycobacterium abscessus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KNU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5289MyabA.00937.a.A1 PW30232 at 24.4 mg/mL against JCSG + E1, 2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5 with 20% ethylene glycol as a cryo-protectant, crystal tracking ID 219633e1, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3647.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.66α = 90
b = 79.08β = 90
c = 86.01γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97946ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.75098.50.04527.526.55595255136-327.064
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7497.60.4953.786.64112

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 REPLACEMENTTHROUGHOUT3knu1.75054992279898.290.17230.17090.1975RANDOM21.637
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]
-0.54-0.220.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.659
r_dihedral_angle_4_deg17.194
r_dihedral_angle_3_deg12.437
r_dihedral_angle_1_deg5.433
r_scangle_it3.976
r_scbond_it2.419
r_mcangle_it1.629
r_angle_refined_deg1.448
r_mcbond_it0.912
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.659
r_dihedral_angle_4_deg17.194
r_dihedral_angle_3_deg12.437
r_dihedral_angle_1_deg5.433
r_scangle_it3.976
r_scbond_it2.419
r_mcangle_it1.629
r_angle_refined_deg1.448
r_mcbond_it0.912
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3352
Nucleic Acid Atoms
Solvent Atoms390
Heterogen Atoms16

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
BOSdata collection
XDSdata reduction