☰ Navigation Tabs
The 1.95 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 6.9 293 30% PEG 8000 w/v, 0.2 M Na acetate, 0.1 M cacodylate buffer, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.04 39.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.4 α = 90 b = 64.75 β = 90 c = 75.78 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 120 IMAGE PLATE RIGAKU RAXIS IV 2005-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 1.95 35.646 88.8 0.075 0.075 9.2 3.1 15108 13324 2 2 18.03
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) 1.95 2.06 49 49 0.378 0.378 2 2 1019
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 1.95 35.65 12666 13324 658 88.21 0.179 0.179 0.177 0.1754 0.233 0.231 RANDOM 14.235
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] -0.06 -0.07 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.428 r_dihedral_angle_4_deg 15.244 r_dihedral_angle_3_deg 14.002 r_dihedral_angle_1_deg 6.2 r_scangle_it 3.459 r_scbond_it 2.185 r_angle_refined_deg 1.446 r_mcangle_it 1.335 r_mcbond_it 0.793 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.428 r_dihedral_angle_4_deg 15.244 r_dihedral_angle_3_deg 14.002 r_dihedral_angle_1_deg 6.2 r_scangle_it 3.459 r_scbond_it 2.185 r_angle_refined_deg 1.446 r_mcangle_it 1.335 r_mcbond_it 0.793 r_nbtor_refined 0.293 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.101 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1702 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 2
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling