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Crystal structure of a substrate-bound full H/ACA RNP from Pyrococcus furiosus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HAX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.9 293 1.5M lithium sulfate, 50mM sodium acetate (pH 4.9), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 189.518 α = 90 b = 189.518 β = 90 c = 279.045 γ = 120
Symmetry Space Group P 64 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 2006-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 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 4.99 50 99.5 0.082 34.4 10.2 13408
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) 5 5.18 99.8 0.481 4.7
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 3HAX 4.99 20 12531 654 99.89 0.32494 0.32281 0.3116 0.36657 0.3427 RANDOM 263.788
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] 10.06 5.03 10.06 -15.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.89 r_dihedral_angle_3_deg 16.73 r_dihedral_angle_4_deg 14.474 r_dihedral_angle_1_deg 4.561 r_scangle_it 0.999 r_angle_refined_deg 0.971 r_scbond_it 0.457 r_mcangle_it 0.335 r_nbtor_refined 0.286 r_mcbond_it 0.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.89 r_dihedral_angle_3_deg 16.73 r_dihedral_angle_4_deg 14.474 r_dihedral_angle_1_deg 4.561 r_scangle_it 0.999 r_angle_refined_deg 0.971 r_scbond_it 0.457 r_mcangle_it 0.335 r_nbtor_refined 0.286 r_mcbond_it 0.185 r_symmetry_vdw_refined 0.173 r_nbd_refined 0.16 r_xyhbond_nbd_refined 0.107 r_symmetry_hbond_refined 0.095 r_chiral_restr 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 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 4572 Nucleic Acid Atoms 1754 Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling