5MOS

Joint X-ray/neutron structure of cationic trypsin in complex with N-amidinopiperidine


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, 16.0-16.5% (w/v) PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.3347.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.903α = 90
b = 58.646β = 90
c = 67.615γ = 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 BIODIFF2014-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.7749PETRA III, EMBL c/o DESYP14 (MX2)
2NUCLEAR REACTORFRM II BEAMLINE BIODIFF2.673, 2.678FRM 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
10.9642.62199.40.03828.438.681132628
21.55088.70.117.5253.131665
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)
10.961.020.5664.38.412
21.51.530.4542.1822.6

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 REPLACEMENT0.9627.4511.36132539664899.40.09340.09290.1044Random selection
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT1.522.15231623158788.550.1670.16630.1796Random 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_d14.047
f_dihedral_angle_d14.047
f_angle_d1.38
f_angle_d1.38
f_chiral_restr0.101
f_chiral_restr0.101
f_plane_restr0.009
f_plane_restr0.009
f_bond_d0.007
f_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1612
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms15

Software

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