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crystal structure of E. coli pseudouridine synthase RluE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KSV PDB entry 1KSV with N-terminal domain removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 294 4 mg/ml protein in 10 mM Tris, pH 7.5, 2mM EDTA and 2mM DTT equilibrated against 22% (w/v) MME PEG 2000, 200 mM ammonium sulfate, 100 mM sodium acetate, crystals were improved by microseeding a solution of 18-22% MME PEG 2000, 200 mM ammonium sulfate, 100 mM sodium acetate and 2 mg/ml protein at pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.95 36.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.31 α = 90 b = 56.78 β = 90 c = 91.31 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 4 double crystal monochrometer 2003-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 1.2 40 98.1 0.063 13.7 4.6 52181 -3 -3 10.3
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 1.24 94 0.713 2.1 3.5 4929
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 PDB entry 1KSV with N-terminal domain removed 1.2 28.08 49576 49576 4982 100 0.152 0.152 0.149 0.1598 0.179 0.1886 RANDOM 11.18
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] -0.02 0.09 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.185 r_dihedral_angle_4_deg 16.964 r_dihedral_angle_3_deg 12.083 r_sphericity_free 7.981 r_dihedral_angle_1_deg 6.227 r_scangle_it 4.705 r_scbond_it 3.851 r_sphericity_bonded 3.75 r_mcangle_it 2.475 r_mcbond_it 2.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.185 r_dihedral_angle_4_deg 16.964 r_dihedral_angle_3_deg 12.083 r_sphericity_free 7.981 r_dihedral_angle_1_deg 6.227 r_scangle_it 4.705 r_scbond_it 3.851 r_sphericity_bonded 3.75 r_mcangle_it 2.475 r_mcbond_it 2.095 r_rigid_bond_restr 2.071 r_angle_refined_deg 1.672 r_angle_other_deg 1.459 r_mcbond_other 0.666 r_symmetry_vdw_other 0.332 r_nbd_refined 0.222 r_nbd_other 0.217 r_xyhbond_nbd_refined 0.214 r_symmetry_vdw_refined 0.19 r_nbtor_refined 0.177 r_chiral_restr 0.119 r_symmetry_hbond_refined 0.094 r_nbtor_other 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1443 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection CNS phasing