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CRYSTAL STRUCTURE OF DOMAIN A OF THERMUS FLAVUS 5S RRNA AND THE CONTRIBUTION OF WATER MOLECULES TO ITS STRUCTURE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RNA NDB ENTRY ARN035 (PDB ENTRY 1RNA)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.6 51.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.1 α = 90 b = 30.1 β = 90 c = 86.8 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 153 IMAGE PLATE MARRESEARCH M 2 1 x-ray 153 IMAGE PLATE MARRESEARCH M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE CONVENTIONAL Mo 0.7107 2 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.9200 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 83.5 2477
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION NDB ENTRY ARN035 (PDB ENTRY 1RNA) 2.4 8 2477 0.18 23.9
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]
RMS Deviations Key Refinement Restraint Deviation n_angle_d 0.068 n_chiral_restr 0.036 n_bond_d 0.025 n_planar_d 0.014 n_hb_or_metal_coord n_sugar_bond_it n_sugar_angle_it n_phos_bond_it n_phos_angle_it n_bond_angle_restr
RMS Deviations Key Refinement Restraint Deviation n_angle_d 0.068 n_chiral_restr 0.036 n_bond_d 0.025 n_planar_d 0.014 n_hb_or_metal_coord n_sugar_bond_it n_sugar_angle_it n_phos_bond_it n_phos_angle_it n_bond_angle_restr n_dihedral_angle_restr n_impr_tor n_sugar_bond_d n_sugar_bond_angle_d n_phos_bond_d n_phos_bond_angle_d n_plane_restr n_singtor_nbd n_multtor_nbd n_xhyhbond_nbd
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 508 Solvent Atoms 158 Heterogen Atoms
Software Software Software Name Purpose AMoRE phasing NUCLSQ refinement XDS data reduction DENZO data reduction