5MM6

Thrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.527720 mM sodium dihydrogen phosphate ph 7.5, 350 mM NaCl, 27% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.753.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.344α = 90
b = 71.649β = 100.48
c = 72.538γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.979ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.2943.57796.30.99916.343.485703
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.291.3793.10.782.363.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.2943.5771.3685676428596.460.12440.12340.1421
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_d18.797
f_angle_d1.067
f_chiral_restr0.088
f_bond_d0.007
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2297
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms74

Software

Software
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata scaling
XDSdata reduction
PHASERphasing