6KD5

Crystal structure of the extracellular domain of MSPL/TMPRSS13 in complex with dec-RVKR-cmk inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ANY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52880.1M HEPES(pH7.5), 2.4M Ammonium Sulfate
Crystal Properties
Matthews coefficientSolvent content
3.1464.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.84α = 90
b = 62.4β = 90
c = 171.63γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702013-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.64099.60.1510.1750.0880.9959.57.219249
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.7299.91.0121.1740.5930.7292.27.3

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 REPLACEMENTTHROUGHOUT2ANY2.639.9917570149399.470.188010.183950.23567RANDOM33.142
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]
2.63-0.05-2.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.441
r_dihedral_angle_3_deg22.088
r_dihedral_angle_4_deg20.214
r_long_range_B_refined9.932
r_long_range_B_other9.93
r_dihedral_angle_1_deg9.707
r_scangle_other6.848
r_mcangle_it5.562
r_mcangle_other5.561
r_scbond_it4.571
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.441
r_dihedral_angle_3_deg22.088
r_dihedral_angle_4_deg20.214
r_long_range_B_refined9.932
r_long_range_B_other9.93
r_dihedral_angle_1_deg9.707
r_scangle_other6.848
r_mcangle_it5.562
r_mcangle_other5.561
r_scbond_it4.571
r_scbond_other4.518
r_mcbond_it3.676
r_mcbond_other3.676
r_angle_refined_deg1.191
r_angle_other_deg1.121
r_chiral_restr0.046
r_gen_planes_refined0.014
r_gen_planes_other0.006
r_bond_refined_d0.004
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2949
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing