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Crystal structure of RNase H1 from halophilic archaeon Halobacterium salinarum NRC-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EHG PDB ENTRY 2EHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 20%(W/V) PEG 8000, Imidazole(pH6.5), 3%(V/V) MPD, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.802 α = 90 b = 115.802 β = 90 c = 38.282 γ = 90
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 BRUKER SMART 6500 2011-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.41 50 99.9 0.074 0.074 31.61 7.4 48997 -3
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 1.41 1.43 98.9 0.381 0.381 3.613 7.1
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 (All) 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 PDB ENTRY 2EHG 1.41 40.94 48893 2472 99.64 0.1734 0.1734 0.1717 0.2066 0.2171 RANDOM 18.1282
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] -0.58 -0.58 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.597 r_dihedral_angle_4_deg 14.214 r_dihedral_angle_3_deg 12.835 r_dihedral_angle_1_deg 5.981 r_scangle_it 5.494 r_scbond_it 3.57 r_mcangle_it 2.529 r_angle_refined_deg 2.41 r_mcbond_it 1.543 r_chiral_restr 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.597 r_dihedral_angle_4_deg 14.214 r_dihedral_angle_3_deg 12.835 r_dihedral_angle_1_deg 5.981 r_scangle_it 5.494 r_scbond_it 3.57 r_mcangle_it 2.529 r_angle_refined_deg 2.41 r_mcbond_it 1.543 r_chiral_restr 0.156 r_bond_refined_d 0.027 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1994 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling