☰ Navigation Tabs
Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DJ0 1DJ0 and 1EHZ experimental model PDB 1EHZ 1DJ0 and 1EHZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 20% PEG 3350, 0.2 M K3 Citrate, 5 mM spermine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.53 65.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.355 α = 90 b = 80.355 β = 90 c = 205.373 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 ADSC QUANTUM 210 2004-01-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.0 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 4 20 99.2 0.172 9.53 7.6 6998 6998
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 4 4.14 97.9 0.531 3.38 4.8 664
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 (All) 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 1DJ0 and 1EHZ 4 20 5809 5809 328 89.24 0.26462 0.26462 0.25946 0.2662 0.35735 0.3513 RANDOM 63.983
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] 0.71 0.36 0.71 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.65 r_dihedral_angle_3_deg 21.798 r_dihedral_angle_4_deg 20.92 r_dihedral_angle_1_deg 6.097 r_mcangle_it 1.378 r_angle_refined_deg 1.327 r_mcbond_it 0.762 r_scangle_it 0.632 r_scbond_it 0.374 r_xyhbond_nbd_refined 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.65 r_dihedral_angle_3_deg 21.798 r_dihedral_angle_4_deg 20.92 r_dihedral_angle_1_deg 6.097 r_mcangle_it 1.378 r_angle_refined_deg 1.327 r_mcbond_it 0.762 r_scangle_it 0.632 r_scbond_it 0.374 r_xyhbond_nbd_refined 0.34 r_nbtor_refined 0.337 r_symmetry_hbond_refined 0.325 r_nbd_refined 0.308 r_symmetry_vdw_refined 0.262 r_metal_ion_refined 0.206 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 1961 Nucleic Acid Atoms 1196 Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling PHASER phasing