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Crystal structure of designed pentatricopeptide repeat protein dPPR-U8C2 in complex with its target RNA U8C2
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 1.8 31.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.433 α = 90 b = 84.782 β = 90 c = 94.358 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 PIXEL DECTRIS PILATUS3 6M 2015-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9806 SSRF BL19U1
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 2.28 40 98.4 26.3 6 18810
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 2.288 38.668 1.37 18753 909 97.48 0.2261 0.2251 0.229 0.2475 0.2535
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 17.075 f_angle_d 1.802 f_chiral_restr 0.113 f_bond_d 0.016 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2860 Nucleic Acid Atoms 208 Solvent Atoms 67 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction HKL-3000 data collection PHASER phasing