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Crystal Structure of an alkaline exonuclease (LHK-Exo) from Laribacter hongkongensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AVQ PDB ENTRY 1AVQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 293 0.1M Tris pH 8.4, 1.0M potassium sodium tartrate tetrahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.33 63.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.939 α = 90 b = 108.939 β = 90 c = 47.647 γ = 120
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 315 2008-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.9 50 95.1 0.084 32.6 7.1 49906 47456 -3
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 1.9 1.97 70.6 0.581 2 5.3 4942
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1AVQ 1.9 50 24394 23585 1268 96.68 0.20632 0.20436 0.24096 0.2316 RANDOM 37.62
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] -1.21 -0.6 -1.21 1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.995 r_dihedral_angle_3_deg 17.523 r_dihedral_angle_4_deg 16.524 r_dihedral_angle_1_deg 5.55 r_scangle_it 4.817 r_scbond_it 3.105 r_mcangle_it 1.905 r_angle_refined_deg 1.629 r_mcbond_it 1.091 r_chiral_restr 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.995 r_dihedral_angle_3_deg 17.523 r_dihedral_angle_4_deg 16.524 r_dihedral_angle_1_deg 5.55 r_scangle_it 4.817 r_scbond_it 3.105 r_mcangle_it 1.905 r_angle_refined_deg 1.629 r_mcbond_it 1.091 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1523 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 2
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling