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Crystal structure of a hypothetical protein from Neisseria gonorrhoeae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 Native protein: Micolytic MCSG1 D8 (1.5 M ammonium sulfate, 100 mM sodium chloride, 100 mM Bis-Tris/HCl, pH 6.5), 25.6 mg/mL NegoA.19190.a.B1.PS38056, cryoprotectant: 25% ethylene glycol, puck MXK4-1, tray 285291d8, I222 crystal form 2 VAPOR DIFFUSION, SITTING DROP 9 289 Iodide soak for phasing: RigakuReagents JCSG+ C10 (10% PEG20000, 2% dioxane, 100 mM Bicine/NaOH, pH 9.0), 25.6 mg/mL NegoA.19190.a.B1.PS38056, crystal soaked in 20% ethylene glycol and 2.5 M sodium iodide, then flash frozen, puck ZDJ2-5, tray 285290 c10, P212121 crystal form
Crystal Properties Matthews coefficient Solvent content 2.17 43 2.04 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.93 α = 90 b = 74.4 β = 90 c = 78.56 γ = 90
Symmetry Space Group I 2 2 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 RAYONIX MX-300 2017-06-23 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD RIGAKU SATURN 944+ 2017-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F 2 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.6 41.459 99.7 0.058 0.063 0.998 16.5 6.056 19646 -3 21.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 98.7 0.592 0.649 0.873 2.78 5.905
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 1.6 41.459 1.36 19645 1900 99.7 0.1842 0.1813 0.1831 0.2102 0.2099 0 30.8044
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 13.049 f_angle_d 1.081 f_chiral_restr 0.078 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1129 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PHASER phasing ARP model building Coot model building REFMAC refinement XDS data reduction PDB_EXTRACT data extraction