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Crystal Structure of RluF in complex with a 22 nucleotide RNA substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GML PDB 2GML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 200 mM Ammonium acetate, 25% PEG-3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 43.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.552 α = 90 b = 84.128 β = 94.87 c = 91.354 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 CCD ADSC QUANTUM 315r 2007-04-18 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 ALS 8.3.1
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 50 99.2 0.121 6.5 3.3 27018
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 3.11 95.1 0.48 2.9
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 2GML 3 49.51 27006 25651 1355 98.7 0.2336 0.23123 0.2369 0.27899 0.286 RANDOM 43.5
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] 0.03 -0.02 -0.12 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.301 r_dihedral_angle_3_deg 18.917 r_dihedral_angle_4_deg 16.454 r_dihedral_angle_1_deg 5.924 r_scangle_it 1.977 r_angle_refined_deg 1.854 r_angle_other_deg 1.221 r_scbond_it 1.123 r_mcangle_it 0.832 r_mcbond_it 0.436
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.301 r_dihedral_angle_3_deg 18.917 r_dihedral_angle_4_deg 16.454 r_dihedral_angle_1_deg 5.924 r_scangle_it 1.977 r_angle_refined_deg 1.854 r_angle_other_deg 1.221 r_scbond_it 1.123 r_mcangle_it 0.832 r_mcbond_it 0.436 r_symmetry_hbond_refined 0.324 r_symmetry_vdw_other 0.31 r_symmetry_vdw_refined 0.217 r_xyhbond_nbd_refined 0.194 r_chiral_restr 0.081 r_mcbond_other 0.078 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7601 Nucleic Acid Atoms 1900 Solvent Atoms 49 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ELVES refinement