4JYT

Crystal Structure of Matriptase in complex with Inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EAX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.32910.1M Tris, 0.2M MgCl2, 20% PEG8000 , pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2645.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.423α = 90
b = 140.658β = 90
c = 51.325γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++MirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
123092.50.05711.72.23364915425
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0795.30.1862.61.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1EAX225.911464777792.460.217420.215830.24755RANDOM15.854
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]
-0.08-0.030.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.073
r_dihedral_angle_4_deg17.579
r_dihedral_angle_3_deg12.475
r_dihedral_angle_1_deg6.688
r_scangle_it2.362
r_scbond_it1.711
r_angle_refined_deg1.477
r_mcangle_it0.936
r_angle_other_deg0.775
r_mcbond_it0.754
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.073
r_dihedral_angle_4_deg17.579
r_dihedral_angle_3_deg12.475
r_dihedral_angle_1_deg6.688
r_scangle_it2.362
r_scbond_it1.711
r_angle_refined_deg1.477
r_mcangle_it0.936
r_angle_other_deg0.775
r_mcbond_it0.754
r_symmetry_vdw_other0.282
r_nbd_refined0.213
r_symmetry_vdw_refined0.212
r_symmetry_hbond_refined0.206
r_nbd_other0.2
r_xyhbond_nbd_refined0.147
r_mcbond_other0.132
r_nbtor_other0.084
r_chiral_restr0.078
r_xyhbond_nbd_other0.024
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbtor_refined
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1858
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms40

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling