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Crystal structure of the 16S rRNA (adenine(1408)-N(1))-methyltransferase W203A mutant with cosubstrate SAM from Catenulisporales acidiphilia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X1O PDB ENTRY 4X1O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 1.85 M Ammonium Sulfate, 0.08 M Tris, pH 8.5, 3.5% DMSO
Crystal Properties Matthews coefficient Solvent content 2.25 45.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.718 α = 90 b = 83.229 β = 90 c = 93.872 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 100 CCD MARMOSAIC 300 mm CCD 2014-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 2.1 50 99.7 0.082 26.9 4 30535
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 99.9 2.1 4
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 PDB ENTRY 4X1O 2.1 29.31 27026 1909 94.48 0.18618 0.18314 0.1923 0.22957 0.2359 RANDOM 50.088
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] -0.13 0.05 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.703 r_dihedral_angle_4_deg 19.911 r_dihedral_angle_3_deg 15.49 r_long_range_B_other 9.088 r_long_range_B_refined 9.081 r_scangle_other 7.016 r_dihedral_angle_1_deg 6.808 r_scbond_it 4.49 r_scbond_other 4.489 r_mcangle_it 4.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.703 r_dihedral_angle_4_deg 19.911 r_dihedral_angle_3_deg 15.49 r_long_range_B_other 9.088 r_long_range_B_refined 9.081 r_scangle_other 7.016 r_dihedral_angle_1_deg 6.808 r_scbond_it 4.49 r_scbond_other 4.489 r_mcangle_it 4.365 r_mcangle_other 4.364 r_mcbond_it 3.031 r_mcbond_other 3.031 r_angle_refined_deg 2.009 r_angle_other_deg 0.915 r_chiral_restr 0.116 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3210 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHENIX phasing HKL-2000 data reduction