☰ Navigation Tabs
Crystal Structure of Piwi/Argonaute/Zwille(PAZ) domain from Thermococcus thioreducens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U04 PDB ENTRY 1U04
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 298 Dioxane, PEG8000, pH 8.5, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.88 34.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.392 α = 90 b = 60.896 β = 90 c = 66.447 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 MARMOSAIC 300 mm CCD 2008-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.94 44.9 81.1 0.046 0.046 30.7 4.9 14536 1.7 3 32.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.94 2.01 59.4 0.32 0.32 3.23 3.7 1048
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1U04 1.94 44.9 17886 14511 730 81.13 0.218 0.216 0.22 0.267 0.2614 RANDOM 34.363
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] 0.32 0.7 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.248 r_dihedral_angle_4_deg 22.26 r_dihedral_angle_3_deg 15.9 r_dihedral_angle_1_deg 8.183 r_scangle_it 4.419 r_scbond_it 2.944 r_mcangle_it 2.276 r_angle_refined_deg 1.772 r_mcbond_it 1.459 r_angle_other_deg 0.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.248 r_dihedral_angle_4_deg 22.26 r_dihedral_angle_3_deg 15.9 r_dihedral_angle_1_deg 8.183 r_scangle_it 4.419 r_scbond_it 2.944 r_mcangle_it 2.276 r_angle_refined_deg 1.772 r_mcbond_it 1.459 r_angle_other_deg 0.991 r_mcbond_other 0.318 r_symmetry_hbond_refined 0.273 r_symmetry_vdw_other 0.25 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.238 r_nbd_other 0.199 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.115 r_nbtor_other 0.09 r_bond_refined_d 0.021 r_xyhbond_nbd_other 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2016 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling