☰ Navigation Tabs
Crystal structure of a tRNA (guanine-N1)-methyltransferase from Anaplasma phagocytophilum bound to S-adenosylhomocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KNU PDB ENTRY 3KNU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 289 AnphA.00316.a.A1 PS00323 at 21 mg/mL with 3 mM SAH against JCSG+ A4: 30% MPD, 20 mM calcium chloride, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 4.54 72.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.11 α = 90 b = 105.11 β = 90 c = 92.25 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944+ VariMax 2012-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.4 50 99.7 0.082 20.95 7.5 20842 20785 -3 40.675
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 99.9 0.536 4.31
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3KNU 2.4 41.92 20749 1064 99.8 0.1767 0.1752 0.2037 0.1807 RANDOM 35.5847
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] -0.71 -0.71 1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.633 r_dihedral_angle_4_deg 16.671 r_dihedral_angle_3_deg 15.345 r_dihedral_angle_1_deg 4.942 r_mcangle_it 3.358 r_mcbond_it 1.994 r_mcbond_other 1.994 r_angle_refined_deg 1.422 r_angle_other_deg 0.744 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.633 r_dihedral_angle_4_deg 16.671 r_dihedral_angle_3_deg 15.345 r_dihedral_angle_1_deg 4.942 r_mcangle_it 3.358 r_mcbond_it 1.994 r_mcbond_other 1.994 r_angle_refined_deg 1.422 r_angle_other_deg 0.744 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1716 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 28
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction