☰ Navigation Tabs
Substrate RNA Positioning in the Archaeal H/ACA Ribonucleoprotein Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EY4 PDB ENTRY 2EY4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 303 50 mM MES, 100 mM NH4COOCH3, 5 mM MgSO4, 1.0 M NaCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 3.89 68.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.561 α = 90 b = 96.561 β = 90 c = 240.978 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 MARMOSAIC 300 mm CCD 2007-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.87 42.52 100 0.11 41.9 15.1 29512 20534 5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.87 2.945 100
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 (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 ENTRY 2EY4 2.87 42.52 29512 20534 1019 79.97 0.25031 0.24783 0.3142 0.30042 0.35 RANDOM 48.255
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] 6.54 6.54 -13.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.831 r_dihedral_angle_3_deg 21.588 r_dihedral_angle_4_deg 15.798 r_dihedral_angle_1_deg 7.092 r_angle_refined_deg 1.725 r_scangle_it 1.547 r_scbond_it 0.876 r_mcangle_it 0.706 r_mcbond_it 0.385 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.831 r_dihedral_angle_3_deg 21.588 r_dihedral_angle_4_deg 15.798 r_dihedral_angle_1_deg 7.092 r_angle_refined_deg 1.725 r_scangle_it 1.547 r_scbond_it 0.876 r_mcangle_it 0.706 r_mcbond_it 0.385 r_nbtor_refined 0.31 r_nbd_refined 0.239 r_symmetry_hbond_refined 0.238 r_symmetry_vdw_refined 0.192 r_xyhbond_nbd_refined 0.181 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 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 3711 Nucleic Acid Atoms 1293 Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing