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Crystal structure of Streptococcus pneumoniae Sp1610, a putative tRNA (m1A22) methyltransferase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 298 2.0M ammonium sulfate, 0.1M tri-sodium citrate pH5.6, 0.2M sodium/potassium tartrate, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3 58.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.807 α = 90 b = 58.668 β = 90 c = 142.995 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.97888, 0.97917, 0.96395 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 71.43 20787
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2 71.43 20787 1064 98.23 0.236 0.234 0.2259 0.289 0.2742 RANDOM 28.211
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] -1.78 -1.32 3.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.732 r_dihedral_angle_3_deg 16.68 r_dihedral_angle_4_deg 15.611 r_dihedral_angle_1_deg 6.075 r_scangle_it 4.809 r_scbond_it 3.081 r_angle_refined_deg 1.695 r_mcangle_it 1.67 r_mcbond_it 0.973 r_chiral_restr 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.732 r_dihedral_angle_3_deg 16.68 r_dihedral_angle_4_deg 15.611 r_dihedral_angle_1_deg 6.075 r_scangle_it 4.809 r_scbond_it 3.081 r_angle_refined_deg 1.695 r_mcangle_it 1.67 r_mcbond_it 0.973 r_chiral_restr 0.13 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1735 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction