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Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EY4 PDB entry 2EY4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 303 2.0mM CoCl2, 30mM CaCl2, 2.0mM Spermine, 2.0M LiCl, pH 6.5, vapor diffusion, hanging drop, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.72 59.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 238.341 α = 90 b = 238.341 β = 90 c = 127.369 γ = 120
Symmetry Space Group P 62 2 2
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 300 mm CCD 2008-03-16 M SINGLE WAVELENGTH 2 1 CCD MARMOSAIC 225 mm CCD 2008-03-16
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID 2 SYNCHROTRON APS BEAMLINE 22-BM APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.65 49.33 22492
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 2EY4 3.65 49.33 22492 1208 97.8 0.277 0.276 0.2361 0.306 0.2574 RANDOM 132.735
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] -6.76 -3.38 -6.76 10.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.603 r_dihedral_angle_4_deg 22.314 r_dihedral_angle_3_deg 21.598 r_dihedral_angle_1_deg 6.922 r_scangle_it 2.27 r_mcangle_it 1.656 r_angle_refined_deg 1.505 r_scbond_it 1.237 r_mcbond_it 0.911 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.603 r_dihedral_angle_4_deg 22.314 r_dihedral_angle_3_deg 21.598 r_dihedral_angle_1_deg 6.922 r_scangle_it 2.27 r_mcangle_it 1.656 r_angle_refined_deg 1.505 r_scbond_it 1.237 r_mcbond_it 0.911 r_nbtor_refined 0.312 r_nbd_refined 0.239 r_symmetry_vdw_refined 0.227 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2989 Nucleic Acid Atoms 1271 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling MOLREP phasing CNS refinement DENZO data reduction PDB_EXTRACT data extraction