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Vibrio cholerae LapD S helix-GGDEF-EAL (apo)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 2.5 M sodium acetate trihydrate, pH 7.0
15% glycerol
Crystal Properties Matthews coefficient Solvent content 2.94 58.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.83 α = 90 b = 129.83 β = 90 c = 114.441 γ = 120
Symmetry Space Group P 32 2 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 PIXEL DECTRIS PILATUS3 6M 2014-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.6309 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.7 19.534 94.6 0.095 0.102 0.037 0.996 14.6 7.3 29068 45.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 95.7 0.414 0.445 0.159 0.922 7.7
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.7 12.69 1.34 28845 1974 94.13 0.2017 0.1987 0.2013 0.2427 0.2445 56.82
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.4272 f_angle_d 0.3663 f_chiral_restr 0.0386 f_plane_restr 0.0025 f_bond_d 0.0013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6486 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHENIX phasing