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STRUCTURE OF TRNA PSI55 PSEUDOURIDINE SYNTHASE (TRUB)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K8W PDB entry 1K8W protein component
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microseeding 7.5 298 AMMONIUM SULFATE, TRIS BUFFER, PEG3350, pH 7.5, temperature 298K, microseeding
Crystal Properties Matthews coefficient Solvent content 3.03 59.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.948 α = 90 b = 94.1 β = 100.36 c = 78.508 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 CCD ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0322 ALS 5.0.1
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 1.9 40.2 0.046 12.4 3.6 51411 28.8
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 1.9 1.97 0.34 2 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1K8W protein component 1.9 40.16 48859 2551 99.43 0.20268 0.20082 0.2032 0.23947 0.2394 RANDOM 20.756
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] -0.04 0.35 -0.43 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.461 r_scangle_it 2.258 r_scbond_it 1.254 r_angle_refined_deg 0.973 r_mcangle_it 0.749 r_mcbond_it 0.387 r_symmetry_vdw_refined 0.191 r_nbd_refined 0.183 r_symmetry_hbond_refined 0.144 r_xyhbond_nbd_refined 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.461 r_scangle_it 2.258 r_scbond_it 1.254 r_angle_refined_deg 0.973 r_mcangle_it 0.749 r_mcbond_it 0.387 r_symmetry_vdw_refined 0.191 r_nbd_refined 0.183 r_symmetry_hbond_refined 0.144 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_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 3930 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing