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Crystal structure of a tRNA (cytidine(34)-2'-O)-methyltransferase bound to S-adenosyl homocysteine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 BupsA.00072.a.A1 PW25076 at 25 mg/mL with 3 mM SAH against Morpheus screen condition G12, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.02 M each carboxylate: sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, sodium oxamate, 0.1 M bicine/Trizma pH 8.5, crystal tracking ID 236960g12, unique puck ID qoj5-3, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.22 44.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.6 α = 90 b = 149.71 β = 90.49 c = 80.3 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX-300 2013-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.15 50 98.1 0.073 13.84 3.9 67356 66051 -3
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 2.15 2.21 97.4 0.461 2.92
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 MOLECULAR REPLACEMENT THROUGHOUT 2.15 44.17 62704 3346 95.73 0.17043 0.1692 0.1758 0.19333 0.1921 RANDOM 31.742
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] 11.72 -7.22 -0.09 -11.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.41 r_dihedral_angle_4_deg 16.358 r_dihedral_angle_3_deg 13.379 r_dihedral_angle_1_deg 5.851 r_mcangle_it 1.994 r_angle_refined_deg 1.42 r_scbond_it 1.303 r_mcbond_it 1.194 r_mcbond_other 1.194 r_angle_other_deg 0.789
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.41 r_dihedral_angle_4_deg 16.358 r_dihedral_angle_3_deg 13.379 r_dihedral_angle_1_deg 5.851 r_mcangle_it 1.994 r_angle_refined_deg 1.42 r_scbond_it 1.303 r_mcbond_it 1.194 r_mcbond_other 1.194 r_angle_other_deg 0.789 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 9167 Nucleic Acid Atoms Solvent Atoms 428 Heterogen Atoms 110
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction