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Crystal structure of Aquifex aeolicus RNase H3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D0A PDB ENTRY 2D0A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 277 0.1M citrate buffer (pH 4.0), 0.2M sodium citrate, 20% w/v polyethylene glycol (PEG) 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.43 64.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.943 α = 90 b = 48.943 β = 90 c = 293.217 γ = 120
Symmetry Space Group P 31 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 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) 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 1.98 50 100 0.104 6.1 21.3 29839 1 1
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 1.98 2.01 100 0.289 21.4
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 PDB ENTRY 2D0A 1.98 48.87 28119 1504 99.51 0.20603 0.20434 0.23844 0.2331 RANDOM 25.683
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] 0.49 0.24 0.49 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.063 r_dihedral_angle_4_deg 23.253 r_dihedral_angle_3_deg 17.136 r_scangle_it 8.259 r_dihedral_angle_1_deg 6.694 r_scbond_it 5.109 r_mcangle_it 3.212 r_mcbond_it 1.925 r_angle_refined_deg 1.049 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.063 r_dihedral_angle_4_deg 23.253 r_dihedral_angle_3_deg 17.136 r_scangle_it 8.259 r_dihedral_angle_1_deg 6.694 r_scbond_it 5.109 r_mcangle_it 3.212 r_mcbond_it 1.925 r_angle_refined_deg 1.049 r_chiral_restr 0.092 r_gen_planes_refined 0.019 r_bond_refined_d 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2063 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms
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