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Joint X-ray/neutron structure of cationic trypsin in complex with 2-aminopyridine
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I8H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, 15.5-16.5% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.33 47.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.989 α = 90 b = 58.537 β = 90 c = 67.618 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 PIXEL DECTRIS PILATUS 6M 2015-06-10 M SINGLE WAVELENGTH 2 1 neutron 295 IMAGE PLATE MAATEL BIODIFF 2015-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.7069 PETRA III, EMBL c/o DESY P14 (MX2) 2 NUCLEAR REACTOR FRM II BEAMLINE BIODIFF 2.675 FRM II BIODIFF
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 0.939 42.662 99.7 0.041 28.59 8.75 141985 2 1.42 25 90.7 0.094 8.493 2.6 38142
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.939 1 0.633 4.29 8.581 2 1.42 1.45 0.414 2.051 2
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MOLECULAR REPLACEMENT 0.939 16.935 1.36 141879 7170 99.74 0.0989 0.0986 0.1044 Random selection NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.42 22.13 38107 1913 90.76 0.1705 0.1699 0.181 Random selection
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 13.953 f_dihedral_angle_d 13.953 f_angle_d 1.234 f_angle_d 1.234 f_chiral_restr 0.098 f_chiral_restr 0.098 f_plane_restr 0.008 f_plane_restr 0.008 f_bond_d 0.007 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1608 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement XDS data reduction HKL-2000 data reduction XDS data scaling HKL-2000 data scaling PHASER phasing Coot model building