☰ Navigation Tabs
Crystal Structure of the C-Terminal RNase III Domain of Human Dicer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JFZ PDB ENTRY 1JFZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 278 1.0M ammonium sulfate, 0.1M TRIS-HCL, 0.01M MGCL2, pH 8.00, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 3.73 67.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.602 α = 90 b = 199.743 β = 90 c = 119.64 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 4 2005-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 50 72223
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1JFZ 2 50 68021 3627 99.7 0.212 0.211 0.2165 0.234 0.2146 RANDOM 40.46
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] -0.14 -2.03 2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.361 r_scangle_it 4.971 r_angle_other_deg 3.576 r_scbond_it 3.026 r_mcangle_it 2.731 r_mcbond_it 1.796 r_angle_refined_deg 1.483 r_symmetry_vdw_other 0.291 r_nbd_other 0.278 r_nbd_refined 0.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.361 r_scangle_it 4.971 r_angle_other_deg 3.576 r_scbond_it 3.026 r_mcangle_it 2.731 r_mcbond_it 1.796 r_angle_refined_deg 1.483 r_symmetry_vdw_other 0.291 r_nbd_other 0.278 r_nbd_refined 0.239 r_symmetry_vdw_refined 0.188 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.176 r_metal_ion_refined 0.158 r_chiral_restr 0.102 r_nbtor_other 0.102 r_bond_refined_d 0.02 r_gen_planes_other 0.01 r_gen_planes_refined 0.008 r_bond_other_d r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4206 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 6
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling