5MON

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)
TypeSourceAccession CodeDetails
experimental modelPDB 4I8H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, 15.5-16.5% (w/v) PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.3347.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.989α = 90
b = 58.537β = 90
c = 67.618γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295PIXELDECTRIS PILATUS 6M2015-06-10MSINGLE WAVELENGTH
21neutron295IMAGE PLATEMAATEL BIODIFF2015-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.7069PETRA III, EMBL c/o DESYP14 (MX2)
2NUCLEAR REACTORFRM II BEAMLINE BIODIFF2.675FRM IIBIODIFF

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
10.93942.66299.70.04128.598.75141985
21.422590.70.0948.4932.638142
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)RedundancyNumber Unique Reflections (All)
10.93910.6334.298.581
21.421.450.4142.0512

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT0.93916.9351.36141879717099.740.09890.09860.1044Random selection
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT1.4222.1338107191390.760.17050.16990.181Random 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
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.953
f_dihedral_angle_d13.953
f_angle_d1.234
f_angle_d1.234
f_chiral_restr0.098
f_chiral_restr0.098
f_plane_restr0.008
f_plane_restr0.008
f_bond_d0.007
f_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1608
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms13

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
HKL-2000data reduction
XDSdata scaling
HKL-2000data scaling
PHASERphasing
Cootmodel building