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Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid (1.54 Angstrom wavelength): Soak in 0.5 mM EGTA and 200 mM K+ at 21 C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZBL PDBID 1ZBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 14% PEG3350, 20% glycerol, 200 mM KI, and 25 mM CaCl2
Crystal Properties Matthews coefficient Solvent content 2.5 50.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.456 α = 90 b = 38.02 β = 96.22 c = 62.071 γ = 90
Symmetry Space Group C 1 2 1
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 RIGAKU SATURN A200 2013-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 1.95 22.01 92.3 0.07 14.1 3.1 12950
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) 1 1.95 2.02 78.1 0.215 3.6 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT PDBID 1ZBL 1.948 22.01 1.37 12947 608 92.14 0.1494 0.147 0.1505 0.1953 0.1978
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 f_dihedral_angle_d 19.92 f_angle_d 1.037 f_chiral_restr 0.057 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1085 Nucleic Acid Atoms 243 Solvent Atoms 164 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing