☰ Navigation Tabs
Crystal structure of Streptococcus pneumoniae Sp1610, a putative tRNA (m1A22) methyltransferase, in complex with S-adenosyl-L-methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 1.6M tri-sodium citrate (pH5.6), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.36 71.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.752 α = 90 b = 142.752 β = 90 c = 148.163 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 210 2008-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3 50 0.087 0.087 22.8 5.7 67466
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3KR9 3 47.46 64055 3411 99.79 0.246 0.244 0.2422 0.296 0.295 RANDOM 83.49
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] 0.28 0.14 0.28 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.657 r_dihedral_angle_3_deg 23.075 r_dihedral_angle_4_deg 20.96 r_dihedral_angle_1_deg 8.108 r_scangle_it 3.805 r_scbond_it 2.213 r_angle_refined_deg 2.081 r_mcangle_it 1.495 r_mcbond_it 0.858 r_symmetry_vdw_refined 0.445
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.657 r_dihedral_angle_3_deg 23.075 r_dihedral_angle_4_deg 20.96 r_dihedral_angle_1_deg 8.108 r_scangle_it 3.805 r_scbond_it 2.213 r_angle_refined_deg 2.081 r_mcangle_it 1.495 r_mcbond_it 0.858 r_symmetry_vdw_refined 0.445 r_nbtor_refined 0.326 r_symmetry_hbond_refined 0.299 r_nbd_refined 0.28 r_xyhbond_nbd_refined 0.21 r_chiral_restr 0.13 r_bond_refined_d 0.019 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13374 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 108
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling SCALA data scaling