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Crystal structure of Tm1865, an Endonuclease V from Thermotoga Maritima
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 Crystallization drop was 1:1 mixture of protein dissolved in 20 mM Tris pH 8.5, 100 mM NaCl and 24 w/v% PEG 1500, 20% glycerol. The crystallization reservoir was 1.5 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.84 33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.571 α = 90 b = 71.966 β = 90 c = 120.266 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 300 mm CCD 2007-06-27 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97876, 0.97860, 0.97243 APS 22-ID
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 2.7 50 99.8 0.131 15.333 5.3 17147
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) 2.7 2.8 99.8 0.453 3.27 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 2.7 50 16183 890 99.77 0.16742 0.16275 0.1756 0.25518 0.2506 RANDOM 28.281
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] -0.38 0.75 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.169 r_dihedral_angle_3_deg 19.993 r_dihedral_angle_4_deg 18.132 r_scangle_it 6.646 r_dihedral_angle_1_deg 6.182 r_scbond_it 4.025 r_mcangle_it 2.583 r_angle_refined_deg 1.635 r_mcbond_it 1.491 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.169 r_dihedral_angle_3_deg 19.993 r_dihedral_angle_4_deg 18.132 r_scangle_it 6.646 r_dihedral_angle_1_deg 6.182 r_scbond_it 4.025 r_mcangle_it 2.583 r_angle_refined_deg 1.635 r_mcbond_it 1.491 r_nbtor_refined 0.326 r_nbd_refined 0.234 r_symmetry_vdw_refined 0.214 r_symmetry_hbond_refined 0.187 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 5291 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing REFMAC refinement PDB_EXTRACT data extraction