☰ Navigation Tabs
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 PEG 400, CaCl2, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.14 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.108 α = 90 b = 46.108 β = 90 c = 33.318 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 RU200
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 40 99.7 0.056 19.9 7 1322 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 3.1 97.9 0.25 8.1 5.1
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 32.6 2 1322 141 99.93 0.26118 0.25529 0.2532 0.32168 0.3108 RANDOM 30.89
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] -0.36 -0.36 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.11 r_dihedral_angle_3_deg 19.573 r_dihedral_angle_4_deg 19.232 r_dihedral_angle_1_deg 6.97 r_scangle_it 1.726 r_angle_refined_deg 1.627 r_scbond_it 1.179 r_mcangle_it 0.848 r_mcbond_it 0.517 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.11 r_dihedral_angle_3_deg 19.573 r_dihedral_angle_4_deg 19.232 r_dihedral_angle_1_deg 6.97 r_scangle_it 1.726 r_angle_refined_deg 1.627 r_scbond_it 1.179 r_mcangle_it 0.848 r_mcbond_it 0.517 r_nbtor_refined 0.313 r_nbd_refined 0.273 r_symmetry_vdw_refined 0.254 r_symmetry_hbond_refined 0.249 r_xyhbond_nbd_refined 0.191 r_chiral_restr 0.088 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 547 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling