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Crystal structure of Trm14 from Pyrococcus furiosus in complex with S-adenosylmethionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TLJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100 mM Tris-acetate, 32% PEG 4000, 15% glycerol, crystal was soaked in crystallization solution containing 1 mM S-adenosylmethionine, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.08 α = 90 b = 45.17 β = 91.79 c = 121.43 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 2011-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00150 SLS X06DA
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 1.95 50 99.5 0.073 18.29 7.1 65622 65283
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 1.95 2 98.9 0.544 3.6 6.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3TLJ 1.95 49.53 65283 62011 3264 100 0.18258 0.18187 0.1682 0.19592 0.1879 RANDOM 29.15
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] -2.1 4.34 -1.04 3.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.013 r_dihedral_angle_4_deg 16.189 r_dihedral_angle_3_deg 15.022 r_dihedral_angle_1_deg 7.171 r_scangle_it 6.534 r_scbond_it 4.178 r_mcangle_it 2.664 r_mcbond_it 1.607 r_angle_refined_deg 1.4 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.013 r_dihedral_angle_4_deg 16.189 r_dihedral_angle_3_deg 15.022 r_dihedral_angle_1_deg 7.171 r_scangle_it 6.534 r_scbond_it 4.178 r_mcangle_it 2.664 r_mcbond_it 1.607 r_angle_refined_deg 1.4 r_chiral_restr 0.124 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 382 Heterogen Atoms 54
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction