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Crystal structure of Trm14 from Pyrococcus furiosus in complex with S-adenosyl-L-homocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other PfTrm14 solved with seleno methionine SAD phasing
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100 mM Tris-acetate, 32% PEG 4000, 15% glycerol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.71 54.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.52 α = 90 b = 45.33 β = 91.23 c = 122.23 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 MARMOSAIC 225 mm CCD 2010-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 2.2 50 99.7 0.108 9.3 3.5 46611 46452
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 2.2 2.3 99.7 0.108 2.7 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PfTrm14 solved with seleno methionine SAD phasing 2.2 49.62 46452 41294 2150 93.51 0.1874 0.18568 0.21987 0.2362 RANDOM 27.077
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] -5.43 1.2 -3.12 8.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.052 r_dihedral_angle_4_deg 19.335 r_dihedral_angle_3_deg 16.747 r_dihedral_angle_1_deg 7.434 r_scangle_it 5.784 r_scbond_it 3.854 r_mcangle_it 2.328 r_angle_refined_deg 1.564 r_mcbond_it 1.431 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.052 r_dihedral_angle_4_deg 19.335 r_dihedral_angle_3_deg 16.747 r_dihedral_angle_1_deg 7.434 r_scangle_it 5.784 r_scbond_it 3.854 r_mcangle_it 2.328 r_angle_refined_deg 1.564 r_mcbond_it 1.431 r_chiral_restr 0.121 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5780 Nucleic Acid Atoms Solvent Atoms 373 Heterogen Atoms 56
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction