3LGA

Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-homocysteine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LHDPDB ENTRY 3LHD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2912.4M ammonium sulfate, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.216α = 90
b = 138.216β = 90
c = 121.119γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rbi-morph mirrors2009-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.98SOLEILPROXIMA 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
12.0534.8699.80.09111.54.816205734.54
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)
2.052.161000.7062.14.823768

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 3LHD2.0534.86153870811699.760.199590.198620.21768RANDOM38.427
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]
0.640.320.64-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.819
r_dihedral_angle_4_deg23.636
r_dihedral_angle_3_deg17.294
r_dihedral_angle_1_deg6.933
r_scangle_it4.94
r_scbond_it3.115
r_mcangle_it1.995
r_angle_refined_deg1.824
r_mcbond_it1.248
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.819
r_dihedral_angle_4_deg23.636
r_dihedral_angle_3_deg17.294
r_dihedral_angle_1_deg6.933
r_scangle_it4.94
r_scbond_it3.115
r_mcangle_it1.995
r_angle_refined_deg1.824
r_mcbond_it1.248
r_nbtor_refined0.31
r_symmetry_vdw_refined0.254
r_nbd_refined0.21
r_chiral_restr0.165
r_xyhbond_nbd_refined0.138
r_symmetry_hbond_refined0.102
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8152
Nucleic Acid Atoms
Solvent Atoms340
Heterogen Atoms124

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling