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Crystal structure of designed pentatricopeptide repeat protein dPPR-U10 in complex with its target RNA U10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PJR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 PEG 3350, Bis-Tris propane, Magnesium chloride, Ethyl Acetate,D-(+)-glucose monohydrate
Crystal Properties Matthews coefficient Solvent content 1.87 34.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.732 α = 90 b = 85.266 β = 90 c = 95.104 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 315r 2014-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4PJR 2.194 38.903 1.33 22260 1088 98.57 0.2527 0.2503 0.2526 0.2994 0.2982
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 17.361 f_angle_d 1.241 f_chiral_restr 0.058 f_bond_d 0.01 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2990 Nucleic Acid Atoms 204 Solvent Atoms 76 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection HKL-2000 data processing PHASER phasing