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Crystal structure of Trm14 from Pyrococcus furiosus in complex with sinefungin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TLJ pdb entry 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 sinefungin, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.66 53.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.245 α = 90 b = 45.064 β = 91.81 c = 121.082 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 2011-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.98000 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 2.27 50 98.7 0.147 8.6 3.8 80676 55944
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 2.27 2.4 92.8 0.643 2.08 3.7
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 pdb entry 3TLJ 2.27 48.02 43175 36169 1908 90.99 0.20474 0.20397 0.2179 0.21892 0.238 RANDOM 24.383
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] 9.15 1.85 -6.02 -3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.082 r_dihedral_angle_4_deg 20.601 r_dihedral_angle_3_deg 17.771 r_dihedral_angle_1_deg 7.904 r_scangle_it 5.28 r_scbond_it 3.483 r_mcangle_it 2.113 r_angle_refined_deg 1.61 r_mcbond_it 1.23 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.082 r_dihedral_angle_4_deg 20.601 r_dihedral_angle_3_deg 17.771 r_dihedral_angle_1_deg 7.904 r_scangle_it 5.28 r_scbond_it 3.483 r_mcangle_it 2.113 r_angle_refined_deg 1.61 r_mcbond_it 1.23 r_chiral_restr 0.111 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 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 5835 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 54
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction