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Crystal Structure of RNase HI from Sulfolobus tokodaii with C-terminal deletion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 20% PEG 3000, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.25 45.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.975 α = 89.72 b = 41.018 β = 89.71 c = 43.534 γ = 86.76
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 210 mirrors 2009-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
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 1.66 50 96.2 0.034 0.031 37.21 3.9 32375 5 5
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 1.66 1.72 94.3 0.218 0.193 6.14 3.9 3175
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2EHG 1.66 20.48 30726 1639 96.36 0.19996 0.19714 0.25048 0.2576 RANDOM 25.003
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 r_dihedral_angle_2_deg 32.083 r_dihedral_angle_3_deg 18.392 r_dihedral_angle_4_deg 17.057 r_scangle_it 7.212 r_dihedral_angle_1_deg 6.546 r_scbond_it 4.436 r_mcangle_it 3.035 r_mcbond_it 1.842 r_angle_refined_deg 1.391 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.083 r_dihedral_angle_3_deg 18.392 r_dihedral_angle_4_deg 17.057 r_scangle_it 7.212 r_dihedral_angle_1_deg 6.546 r_scbond_it 4.436 r_mcangle_it 3.035 r_mcbond_it 1.842 r_angle_refined_deg 1.391 r_chiral_restr 0.115 r_gen_planes_refined 0.017 r_bond_refined_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2244 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms
Software Software Software Name Purpose BL38 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling