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The 1.6 A crystal structure of Vibrio cholerae extracellular endonuclease I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 25% PEG 4000, 0.1 M Na acetate pH 4.6, 0.3 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.03 39.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.52 α = 90 b = 64.16 β = 90 c = 75.57 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 IMAGE PLATE MARRESEARCH 2005-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM1A 0.873 ESRF BM1A
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 1.6 25.384 100 0.055 0.055 9.1 4.5 26728 2 2 16.34
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) 1.6 1.69 100 100 0.389 0.389 1.9 4.6 3846
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 1ouo 1.6 25.38 26747 26725 1344 99.92 0.224 0.224 0.222 0.2216 0.255 0.2545 RANDOM 17.676
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.96 r_dihedral_angle_3_deg 13.706 r_dihedral_angle_4_deg 12.857 r_dihedral_angle_1_deg 9.053 r_scangle_it 3.256 r_scbond_it 2.258 r_angle_refined_deg 1.486 r_mcangle_it 1.396 r_mcbond_it 0.88 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.96 r_dihedral_angle_3_deg 13.706 r_dihedral_angle_4_deg 12.857 r_dihedral_angle_1_deg 9.053 r_scangle_it 3.256 r_scbond_it 2.258 r_angle_refined_deg 1.486 r_mcangle_it 1.396 r_mcbond_it 0.88 r_nbtor_refined 0.305 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1722 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 1
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling