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Structure of Vibrio cholerae VesB protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EAX PDB ENTRY 1EAX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 277 0.1 M Tris-HCl, pH 9.0, 3.0 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.43 64.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.57 α = 90 b = 121.57 β = 90 c = 71.31 γ = 90
Symmetry Space Group P 42 21 2
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 315r 2010-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9999 ALS 8.2.2
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 2.4 46.3 99.5 0.065 20.43 6.31 21460 21358 -3 56.776
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 2.4 2.46 99.9 1.073 2.33 6.48 1550
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MR-SAD THROUGHOUT PDB ENTRY 1EAX 2.4 46.3 20306 1070 99.53 0.1896 0.1872 0.1914 0.2363 0.2311 RANDOM 59.7818
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] 0.3 0.3 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.664 r_dihedral_angle_4_deg 19.144 r_dihedral_angle_3_deg 14.366 r_dihedral_angle_1_deg 6.153 r_mcangle_it 1.941 r_angle_refined_deg 1.466 r_mcbond_other 1.192 r_mcbond_it 1.191 r_angle_other_deg 0.781 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.664 r_dihedral_angle_4_deg 19.144 r_dihedral_angle_3_deg 14.366 r_dihedral_angle_1_deg 6.153 r_mcangle_it 1.941 r_angle_refined_deg 1.466 r_mcbond_other 1.192 r_mcbond_it 1.191 r_angle_other_deg 0.781 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2465 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction PHASER phasing