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Crystal structure of a catalytically active substrate-bound box C/D RNP from Sulfolobus solfataricus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ICX PDB ENTRIES 3ICX, 3ID6, 3ID5 experimental model PDB 3ID6 PDB ENTRIES 3ICX, 3ID6, 3ID5 experimental model PDB 3ID5 PDB ENTRIES 3ICX, 3ID6, 3ID5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 2.0M (NH4)2SO4, 2% PEG 400, 10mM MgCl2, 0.1M HEPES-Na (pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.5 64.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 241.199 α = 90 b = 241.199 β = 90 c = 145.408 γ = 90
Symmetry Space Group P 41 21 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 RAYONIX MX-225 2010-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9789 SSRF BL17U
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 3.15 20 95.1 0.095 16.3 4.3 70682
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) 3.15 3.2 94.4 0.536 2.3 4
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 ENTRIES 3ICX, 3ID6, 3ID5 3.15 19.91 66836 3540 95.11 0.24928 0.24776 0.2429 0.27761 0.2726 RANDOM 88.687
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] -1.18 -1.18 2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.77 r_dihedral_angle_3_deg 20.228 r_dihedral_angle_4_deg 16.803 r_dihedral_angle_1_deg 6.538 r_scangle_it 1.599 r_angle_refined_deg 1.324 r_mcangle_it 1.066 r_scbond_it 0.92 r_mcbond_it 0.698 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.77 r_dihedral_angle_3_deg 20.228 r_dihedral_angle_4_deg 16.803 r_dihedral_angle_1_deg 6.538 r_scangle_it 1.599 r_angle_refined_deg 1.324 r_mcangle_it 1.066 r_scbond_it 0.92 r_mcbond_it 0.698 r_chiral_restr 0.094 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 17247 Nucleic Acid Atoms 2721 Solvent Atoms Heterogen Atoms 78
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling