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Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20% PEG 3350, 0.2 M K3 Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.41 63.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.278 α = 90 b = 128.585 β = 90 c = 159.256 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 ADSC QUANTUM 210 2004-01-23 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 3.5 50 100 0.236 6.99 5.7 25523 25523
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) 3.5 3.63 99.9 0.722 2.42 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.5 20 21541 21541 2384 94.09 0.24936 0.24601 0.2265 0.27912 0.2502 RANDOM 37.066
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] -0.79 -0.34 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.68 r_dihedral_angle_4_deg 17.399 r_dihedral_angle_3_deg 16.62 r_scangle_it 2.697 r_mcangle_it 2.428 r_scbond_it 1.653 r_mcbond_it 1.315 r_angle_refined_deg 1.241 r_dihedral_angle_1_deg 1.046 r_nbtor_refined 0.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.68 r_dihedral_angle_4_deg 17.399 r_dihedral_angle_3_deg 16.62 r_scangle_it 2.697 r_mcangle_it 2.428 r_scbond_it 1.653 r_mcbond_it 1.315 r_angle_refined_deg 1.241 r_dihedral_angle_1_deg 1.046 r_nbtor_refined 0.335 r_nbd_refined 0.277 r_symmetry_vdw_refined 0.253 r_xyhbond_nbd_refined 0.176 r_metal_ion_refined 0.14 r_chiral_restr 0.074 r_symmetry_hbond_refined 0.045 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 8318 Nucleic Acid Atoms 1441 Solvent Atoms Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling PHASER phasing