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Crystal structure of DUF358 protein reveals a putative SPOUT-class rRNA methyltransferase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 PEG, Mg, Tris, Ammonium Fluoride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.07 40.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.288 α = 90 b = 48.133 β = 126.09 c = 62.362 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 210 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 0.9797, 0.9799, 0.95 NSLS X12C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.55 50 85.4 0.038 36.1 3.4 25283
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.55 1.61 56.2 0.321 2.5 2.8
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 1.55 34.06 25283 1356 90.49 0.19193 0.18952 0.1993 0.23682 0.2498 RANDOM 33.53
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] 3.49 -0.37 -1.17 -2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.498 r_dihedral_angle_4_deg 14.744 r_dihedral_angle_3_deg 14.689 r_dihedral_angle_1_deg 6.123 r_scangle_it 4.225 r_scbond_it 2.829 r_mcangle_it 1.647 r_angle_refined_deg 1.644 r_mcbond_it 1.169 r_symmetry_vdw_refined 0.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.498 r_dihedral_angle_4_deg 14.744 r_dihedral_angle_3_deg 14.689 r_dihedral_angle_1_deg 6.123 r_scangle_it 4.225 r_scbond_it 2.829 r_mcangle_it 1.647 r_angle_refined_deg 1.644 r_mcbond_it 1.169 r_symmetry_vdw_refined 0.346 r_nbtor_refined 0.315 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.217 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.106 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1706 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 22
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling