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Crystal structure of the catalytic domain of E. coli pseudouridine synthase RluC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V9K PDB ENTRY 1V9K (molecule A)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 Bicine, sodium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.26 45.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.307 α = 90 b = 97.307 β = 90 c = 86.237 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 93 IMAGE PLATE MARRESEARCH mirrors 1998-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
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 2.2 30 100 0.067 38.4 14 24381 24381
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 2.2 2.28 100 0.441 6.3
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 (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 1V9K (molecule A) 2.2 30 24336 23094 1242 99.94 0.18805 0.18462 0.1831 0.25372 0.2498 RANDOM 33.656
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] 0.08 0.04 0.08 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.194 r_dihedral_angle_4_deg 20.938 r_dihedral_angle_3_deg 15.222 r_dihedral_angle_1_deg 7.376 r_scangle_it 4.888 r_scbond_it 3.176 r_mcangle_it 2.061 r_angle_refined_deg 1.906 r_mcbond_it 1.311 r_symmetry_hbond_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.194 r_dihedral_angle_4_deg 20.938 r_dihedral_angle_3_deg 15.222 r_dihedral_angle_1_deg 7.376 r_scangle_it 4.888 r_scbond_it 3.176 r_mcangle_it 2.061 r_angle_refined_deg 1.906 r_mcbond_it 1.311 r_symmetry_hbond_refined 0.311 r_nbtor_refined 0.301 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.209 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.127 r_bond_refined_d 0.022 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3608 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing