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Structure of WRN RQC domain bound to double-stranded DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 293 20% PEG 4000, 0.2M sodium acetate, 0.1M CAPS-NaOH, pH 9, VAPOR DIFFUSION, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.077 α = 90 b = 84.077 β = 90 c = 145.291 γ = 90
Symmetry Space Group P 43 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 90 CCD Bruker DIP-6040 2007-09-30 M SINGLE WAVELENGTH 2 2 x-ray 90 CCD RAYONIX MX225HE 2008-07-19 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU 2 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0057, 1.0090, 1.0257 SPring-8 BL41XU
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 1.9 20 100 0.043 14.7 9.7 41719
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) 1,2 1.9 1.97 99.9 0.488 6.2 9.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.9 20 39605 2107 99.88 0.21339 0.21177 0.2219 0.24354 0.2582 RANDOM 41.246
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] 1.6 1.6 -3.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.188 r_dihedral_angle_3_deg 15.281 r_dihedral_angle_4_deg 12.815 r_dihedral_angle_1_deg 5.44 r_scangle_it 2.308 r_scbond_it 1.491 r_angle_refined_deg 1.409 r_mcangle_it 1.038 r_mcbond_it 0.614 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.188 r_dihedral_angle_3_deg 15.281 r_dihedral_angle_4_deg 12.815 r_dihedral_angle_1_deg 5.44 r_scangle_it 2.308 r_scbond_it 1.491 r_angle_refined_deg 1.409 r_mcangle_it 1.038 r_mcbond_it 0.614 r_nbtor_refined 0.298 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.155 r_symmetry_vdw_refined 0.153 r_chiral_restr 0.094 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1776 Nucleic Acid Atoms 568 Solvent Atoms 338 Heterogen Atoms 8
Software Software Software Name Purpose HKL-2000 data collection SHARP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling