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Crystal structure of TrmN from Thermus thermophilus
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 3.5 293 100 mM citrate/phosphate, 15% PEG 6000, 200 mM NaCl, 100 mM sodium citrate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 46.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.86 α = 90 b = 65.86 β = 90 c = 144.55 γ = 120
Symmetry Space Group P 32 2 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 2010-08-27 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 2.05 50 100 0.101 22.4 21.3 23538 23534
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 2.05 2.1 100 0.525 7.37 22.1
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 2.05 44.77 23534 22355 1177 100 0.15707 0.15423 0.1673 0.21176 0.2201 RANDOM 31.969
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] 0.1 0.05 0.1 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.362 r_dihedral_angle_4_deg 20.992 r_dihedral_angle_3_deg 16.289 r_dihedral_angle_1_deg 6.753 r_scangle_it 6.092 r_scbond_it 3.841 r_mcangle_it 2.477 r_angle_refined_deg 1.516 r_mcbond_it 1.455 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.362 r_dihedral_angle_4_deg 20.992 r_dihedral_angle_3_deg 16.289 r_dihedral_angle_1_deg 6.753 r_scangle_it 6.092 r_scbond_it 3.841 r_mcangle_it 2.477 r_angle_refined_deg 1.516 r_mcbond_it 1.455 r_chiral_restr 0.132 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 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 2595 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement