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Crystal structure of an H/ACA box RNP from Pyrococcus furiosus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EY4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 303 30% MPD, 35mM CH3COOMg, 10mM ATP, 50mM cacodylate , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.28 46.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.031 α = 90 b = 90.95 β = 90 c = 114.064 γ = 90
Symmetry Space Group P 21 21 21
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 2006-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 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 2.3 20 99.7 0.055 38 6.8 39340 39234 -3
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 2.3 2.34 100 0.331 6.7 7.3 1950
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2EY4 2.3 20 37072 36983 1914 99.76 0.23984 0.23984 0.23786 0.2295 0.27807 0.2698 RANDOM 43.191
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] -0.27 2.4 -2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.482 r_dihedral_angle_4_deg 15.315 r_dihedral_angle_3_deg 14.902 r_dihedral_angle_1_deg 4.815 r_angle_refined_deg 1.045 r_scangle_it 0.641 r_scbond_it 0.379 r_mcangle_it 0.341 r_nbtor_refined 0.288 r_mcbond_it 0.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.482 r_dihedral_angle_4_deg 15.315 r_dihedral_angle_3_deg 14.902 r_dihedral_angle_1_deg 4.815 r_angle_refined_deg 1.045 r_scangle_it 0.641 r_scbond_it 0.379 r_mcangle_it 0.341 r_nbtor_refined 0.288 r_mcbond_it 0.193 r_nbd_refined 0.155 r_symmetry_vdw_refined 0.134 r_symmetry_hbond_refined 0.134 r_xyhbond_nbd_refined 0.111 r_chiral_restr 0.081 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4512 Nucleic Acid Atoms 1235 Solvent Atoms 118 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing