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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 2HVY PDB entry 2HVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 303 0.8 M KCl, 0.15 M Mg Acetate, 8% (w/v) PEG 6000, pH 6.5, vapor diffusion, hanging drop, temperature 303K
Crystal Properties Matthews coefficient Solvent content 3.16 61.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.013 α = 90 b = 63.026 β = 90 c = 85.447 γ = 90
Symmetry Space Group P 21 21 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 2008-12-12 M SINGLE WAVELENGTH 2 1 CCD MARMOSAIC 225 mm CCD 2008-12-12
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) 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 2.15 50 91.3 0.079 20.968 6.1 51141
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 2.15 2.23 51.1 0.592 1.8 2806
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2HVY 2.35 46.52 42200 1807 98.73 0.218 0.217 0.248 0.2417 RANDOM 37.351
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] -1.18 0.17 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.184 r_dihedral_angle_4_deg 17.943 r_dihedral_angle_3_deg 17.364 r_dihedral_angle_1_deg 5.606 r_scangle_it 2.457 r_scbond_it 1.516 r_angle_refined_deg 1.397 r_mcangle_it 0.94 r_mcbond_it 0.467 r_metal_ion_refined 0.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.184 r_dihedral_angle_4_deg 17.943 r_dihedral_angle_3_deg 17.364 r_dihedral_angle_1_deg 5.606 r_scangle_it 2.457 r_scbond_it 1.516 r_angle_refined_deg 1.397 r_mcangle_it 0.94 r_mcbond_it 0.467 r_metal_ion_refined 0.376 r_nbtor_refined 0.295 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.147 r_symmetry_vdw_refined 0.11 r_chiral_restr 0.077 r_symmetry_hbond_refined 0.057 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3964 Nucleic Acid Atoms 1515 Solvent Atoms 99 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction