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Crystal structure of RtcA, the RNA 3'-terminal phosphate cyclase from Pyrococcus horikoshii, in complex with rACAAA3'phosphate and adenine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4O89 PDB ENTRY 4O89
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M proline, 0.1 M HEPES pH 7.5, 10% PEG 3350, cryoprotected by supplementing with 30% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.77 67.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.921 α = 90 b = 110.261 β = 90 c = 127.648 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 MARMOSAIC 300 mm CCD 2013-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97934 APS 23-ID-B
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 2.04 50 100 7.4 75635 75619
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.08 100 2 7.4
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 4O89 2.04 46.14 1.35 71784 71772 1968 94.42 0.16 0.1597 0.1587 0.1634 0.1982 0.2021 thin shells
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.933 f_angle_d 1.363 f_chiral_restr 0.082 f_bond_d 0.012 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5248 Nucleic Acid Atoms 218 Solvent Atoms 610 Heterogen Atoms 53
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling