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THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH A 16NT DNA DUPLEX.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W9H PDB ENTRY 1W9H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.6 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.838 α = 75.8 b = 61.384 β = 75.86 c = 103.54 γ = 79.47
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 ADSC CCD 2005-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 32.72 95.9 0.05 9.62 2.09 89928 25.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 95.5 0.42 1.6 2.09
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 1W9H 1.9 98.06 89899 4463 95.9 0.207 0.205 0.2037 0.243 0.2412 RANDOM 33.18
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] -0.998 0.004 0.604 1.433 -0.516 -0.478
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.156 r_dihedral_angle_4_deg 20.451 r_dihedral_angle_3_deg 16.316 r_dihedral_angle_1_deg 6.233 r_scangle_it 3.828 r_scbond_it 2.624 r_mcangle_it 1.987 r_angle_refined_deg 1.766 r_mcbond_it 1.241 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.156 r_dihedral_angle_4_deg 20.451 r_dihedral_angle_3_deg 16.316 r_dihedral_angle_1_deg 6.233 r_scangle_it 3.828 r_scbond_it 2.624 r_mcangle_it 1.987 r_angle_refined_deg 1.766 r_mcbond_it 1.241 r_nbtor_refined 0.309 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.191 r_symmetry_vdw_refined 0.19 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6370 Nucleic Acid Atoms 452 Solvent Atoms 411 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing