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Crystal structure of 2'-5' RNA ligase from Pyrococcus horikoshii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IUH PDB entry 1iuh
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 Ammonium acetate, Sodium acetate, PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.5 α = 90 b = 45.7 β = 90 c = 97.6 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 2004-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 0.97950 SPring-8 BL44B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.94 50 99.9 0.047 0.047 16.5 7 14330 14330 -3 50.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.94 2.01 99.6 0.384 0.384 6.6 1394
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 1iuh 1.94 10 14194 12780 1414 100 0.21584 0.21047 0.2195 0.26487 0.268 RANDOM 33.802
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] 1.29 -0.99 -0.3
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.231 r_dihedral_angle_1_deg 5.898 r_scbond_it 4.291 r_mcangle_it 2.848 r_angle_refined_deg 1.966 r_mcbond_it 1.602 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.212 r_chiral_restr 0.156
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.231 r_dihedral_angle_1_deg 5.898 r_scbond_it 4.291 r_mcangle_it 2.848 r_angle_refined_deg 1.966 r_mcbond_it 1.602 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.212 r_chiral_restr 0.156 r_symmetry_hbond_refined 0.143 r_bond_refined_d 0.027 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1488 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing