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Structure of Arabidopsis HYL1 and its molecular implications for miRNA processing
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DI2 PDB ENTRY 1DI2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 PEG8000, AS, Cacodylate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.62 α = 90 b = 47.62 β = 90 c = 115.377 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.2 40 97.9 0.101 19.9 7.7 3783 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.3 0.975 4.7 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1DI2 3.2 36.72 2 3783 401 98.45 0.21463 0.2044 0.21 0.31724 0.3151 RANDOM 67.858
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] -0.17 -0.17 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.657 r_dihedral_angle_3_deg 23.315 r_dihedral_angle_4_deg 21.599 r_dihedral_angle_1_deg 6.875 r_scangle_it 1.631 r_angle_refined_deg 1.619 r_scbond_it 0.937 r_mcangle_it 0.883 r_mcbond_it 0.497 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.657 r_dihedral_angle_3_deg 23.315 r_dihedral_angle_4_deg 21.599 r_dihedral_angle_1_deg 6.875 r_scangle_it 1.631 r_angle_refined_deg 1.619 r_scbond_it 0.937 r_mcangle_it 0.883 r_mcbond_it 0.497 r_nbtor_refined 0.318 r_nbd_refined 0.264 r_symmetry_hbond_refined 0.236 r_symmetry_vdw_refined 0.224 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.107 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1716 Nucleic Acid Atoms 422 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling