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Structure of E. coli Isopentenyl-tRNA transferase in complex with E. coli tRNA(Phe)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D3Q 3D3Q, 1TTT experimental model PDB 1TTT 3D3Q, 1TTT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 PEG 4K 15%, 0.2M CaCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.24 α = 90 b = 91.26 β = 90 c = 152.36 γ = 90
Symmetry Space Group P 21 21 21
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 325 mm CCD Double crystal monochromator, Si(111) 2008-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 0.97 MAX II I911-3
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 2.5 78.29 99.8 0.097 6.8 6.5 43836 43749 -3 -3 51
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) 1 2.5 2.6 100 0.493 2.14
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3D3Q, 1TTT 2.5 30 -3 43779 40403 2133 97.16 0.24517 0.24517 0.24389 0.2368 0.26822 0.2919 RANDOM 22.657
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] 0.3 1.46 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.731 r_dihedral_angle_4_deg 17.201 r_dihedral_angle_3_deg 16.788 r_mcangle_it 6.154 r_dihedral_angle_1_deg 5.849 r_scangle_it 5.707 r_mcbond_it 4.415 r_scbond_it 4.344 r_mcbond_other 1.369 r_angle_refined_deg 1.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.731 r_dihedral_angle_4_deg 17.201 r_dihedral_angle_3_deg 16.788 r_mcangle_it 6.154 r_dihedral_angle_1_deg 5.849 r_scangle_it 5.707 r_mcbond_it 4.415 r_scbond_it 4.344 r_mcbond_other 1.369 r_angle_refined_deg 1.279 r_angle_other_deg 0.875 r_chiral_restr 0.059 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4783 Nucleic Acid Atoms 3055 Solvent Atoms 73 Heterogen Atoms 22
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling