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Crystal structure of Treponema pallidum Tp0751 (Pallilysin)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 291 0.1 M sodium acetate pH 5.4, 1.6 M sodium formate
Crystal Properties Matthews coefficient Solvent content 2.82 56.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.72 α = 90 b = 144.72 β = 90 c = 152.61 γ = 120
Symmetry Space Group P 31 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 CCD RAYONIX MX300HE ultra-low expansion (ULE) titanium siliicate flat mirror with Pt, Uncoated, and Pd strips 2015-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.984 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.15 72.36 99.9 0.122 0.993 10.7 7.5 100394 29.4
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 2.15 2.19 100 0.719 2.7 7.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 2.15 65.383 1.36 100350 4992 99.89 0.2465 0.2392 0.2413 0.2764 0.2745 Random selection 44.3369
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 14.796 f_angle_d 0.642 f_chiral_restr 0.025 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8983 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction PHENIX phasing