3NPS

Crystal structure of membrane-type serine protease 1 (MT-SP1) in complex with the Fab Inhibitor S4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BN9PDB ENTRIES: 3BN9, 2JB5, 3KDM
experimental modelPDB 2JB5PDB ENTRIES: 3BN9, 2JB5, 3KDM
experimental modelPDB 3KDMPDB ENTRIES: 3BN9, 2JB5, 3KDM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
129850 mM Tris, 100 mM NaCl, 5% glycerol, no buffer was added for crystallization, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2745.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.161α = 90
b = 83.988β = 91.45
c = 101.394γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MIRRORS2010-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.443.39384.50.058163.788531119.6
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)
11.41.46800.17683.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES: 3BN9, 2JB5, 3KDM1.528.648794388531444784.50.190.1880.228RANDOM23.94
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
r_dihedral_angle_2_deg37.266
r_dihedral_angle_3_deg13.609
r_dihedral_angle_4_deg13.004
r_dihedral_angle_1_deg6.638
r_scangle_it3.758
r_scbond_it2.452
r_mcangle_it1.632
r_angle_refined_deg1.606
r_mcbond_it0.952
r_chiral_restr0.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.266
r_dihedral_angle_3_deg13.609
r_dihedral_angle_4_deg13.004
r_dihedral_angle_1_deg6.638
r_scangle_it3.758
r_scbond_it2.452
r_mcangle_it1.632
r_angle_refined_deg1.606
r_mcbond_it0.952
r_chiral_restr0.113
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5157
Nucleic Acid Atoms
Solvent Atoms676
Heterogen Atoms46

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction