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Room-temperature X-ray structure of D132N Bacillus halodurans RNase H1 in complex with RNA/DNA duplex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G8U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES pH 7.5, 0.2 M NaCl, and 12-16% PEG 10,000
Crystal Properties Matthews coefficient Solvent content 2.41 49.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.184 α = 90 b = 37.743 β = 96.33 c = 62.629 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 293 PIXEL DECTRIS EIGER R 4M 2024-07-08 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) Rpim I (All) CC (Half) 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 1.8 62.2 96.8 0.088 0.052 0.949 13.6 4.1 17367
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.87 94.1 0.678 0.385 0.638 1.04 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 23.53 1.34 17340 860 96.74 0.1866 0.185 0.1872 0.2163 0.2196 random
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 16.723 f_angle_d 1.533 f_chiral_restr 0.093 f_bond_d 0.016 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1089 Nucleic Acid Atoms 249 Solvent Atoms 50 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction CrysalisPro data reduction Aimless data scaling PHASER phasing