☰ Navigation Tabs
The structure of the monoclinic crystal form of the type II ribosome inactivating protein from Winter Aconite Eranthis hyemalis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M2T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 The protein was concentrated to 4 mg/ml for crystallisation screening using MRC MAXI 48-well plates (Molecular Dimensions). A well volume of 200 uL was used and the drops were made with 1 uL of protein and 1 uL of well solution. A crystal was obtained after 24 weeks at room temperature in condition D10 of the PACT Premier screen (0.2 M magnesium chloride, 0.1 M Tris pH 8, 20 % PEG 6000).
Crystal Properties Matthews coefficient Solvent content 2.69 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.15 α = 90 b = 93.17 β = 96.38 c = 70.14 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2015-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9795 Diamond I04-1
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 1.4 28.73 95.5 0.079 0.095 0.993 7.5 3 110338
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 1.4 1.53 82.7 0.648 0.842 0.75 1 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.4 28.73 104912 5426 95.5 0.177 0.176 0.213 0.2134 Random
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3919 Nucleic Acid Atoms Solvent Atoms 807 Heterogen Atoms 120
Software Software Software Name Purpose Servalcat refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing