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Crystal Structure of human Hiwi1 PAZ domain (residues 277-399) in complex with 14-mer RNA (12-bp + 2-nt overhang) containing 2'-OH at its 3'-end
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Hiwi1(V361M)PAZ domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 277 1-5% PEG3350, 50 mM NaCl,
50 mM Na-acetate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.91 35.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.303 α = 90 b = 44.303 β = 90 c = 147.707 γ = 90
Symmetry Space Group P 41 2 2
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 QUANTUM 315 Cryogenically-cooled double crystal Si(111) monochromator. 2010-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
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 2.8 20 96.6 0.096 14.8 4.1 3966
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) 2.8 2.9 78.7 0.361 1.9 2.8
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 THROUGHOUT Hiwi1(V361M)PAZ domain 2.801 15 3713 177 96.93 0.24494 0.24261 0.2399 0.29701 0.2913 RANDOM 45.282
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] 0.99 0.99 -1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.897 r_dihedral_angle_3_deg 13.561 r_dihedral_angle_1_deg 4.093 r_dihedral_angle_4_deg 3.325 r_angle_refined_deg 0.849 r_scangle_it 0.475 r_mcangle_it 0.276 r_scbond_it 0.262 r_mcbond_it 0.149 r_chiral_restr 0.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.897 r_dihedral_angle_3_deg 13.561 r_dihedral_angle_1_deg 4.093 r_dihedral_angle_4_deg 3.325 r_angle_refined_deg 0.849 r_scangle_it 0.475 r_mcangle_it 0.276 r_scbond_it 0.262 r_mcbond_it 0.149 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 871 Nucleic Acid Atoms 292 Solvent Atoms 22 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling