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Crystal Structure of the VPA0106 protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium Target VpR106.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch crystallization under oil 6 291 20% PEG 4000, 0.1M sodium nitrate, 0.1M MES, pH 6.0, Microbatch crystallization under oil, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.79 55.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.445 α = 60.61 b = 96.32 β = 80.87 c = 100.54 γ = 86.55
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 4 2011-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97898 NSLS X4A
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 2.083 50 95.6 0.048 13.3 1.4 198295 188380 25.05
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 2.1 2.18 79.8 0.205 2.8 1.4 19654
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.083 46.958 1.11 188331 9413 94.85 0.195 0.194 0.1794 0.216 0.2017 32.622
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] -5.148 0.733 0.897 0.266 2.341 4.881
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.851 f_angle_d 1.403 f_chiral_restr 0.104 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9549 Nucleic Acid Atoms Solvent Atoms 780 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling SHELXS phasing