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Structural adaptation of endonuclease I from the cold-adapted and halophilic bacterium Vibrio salmonicida
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OUO PDB ENTRY 1OUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 298 30 % PEG 3350, 0.1 M Tris, 0.25 M sodium acetate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.02 39.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.078 α = 90 b = 44.948 β = 92.66 c = 51.746 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 210 2005-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0707 ESRF ID29
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 1.5 33.923 99.3 0.047 0.047 9.4 4 31040 30823 2 10.24
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 1.5 1.58 97.6 0.074 0.074 14 3.7
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 (All) 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 THROUGHOUT PDB ENTRY 1OUO 1.5 33.92 31040 30823 1549 99.3 0.167 0.167 0.166 0.1627 0.185 0.1784 RANDOM 10.917
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] -0.11 -0.04 -0.11 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.534 r_dihedral_angle_4_deg 14.561 r_dihedral_angle_3_deg 10.953 r_dihedral_angle_1_deg 5.771 r_scangle_it 2.897 r_scbond_it 1.797 r_mcangle_it 1.207 r_angle_refined_deg 1.142 r_mcbond_it 0.75 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.534 r_dihedral_angle_4_deg 14.561 r_dihedral_angle_3_deg 10.953 r_dihedral_angle_1_deg 5.771 r_scangle_it 2.897 r_scbond_it 1.797 r_mcangle_it 1.207 r_angle_refined_deg 1.142 r_mcbond_it 0.75 r_nbtor_refined 0.305 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.093 r_symmetry_hbond_refined 0.083 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1704 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction SCALA data scaling MOLREP phasing