6KBR

Crystal structure of Human KLK4 and SPINK2 derived KLK4 inhibitor complex


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Lithium chloride, polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
1.9235.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.208α = 90
b = 41.62β = 91.58
c = 43.59γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2017-04-26MSINGLE 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)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
11.972.57799.60.0998.83.420687
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)
11.91.940.245

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 REPLACEMENTTHROUGHOUT2BDG272.5771690189799.720.187470.185410.22584RANDOM10.645
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.477
r_dihedral_angle_4_deg19.053
r_dihedral_angle_3_deg15.181
r_dihedral_angle_1_deg7.107
r_long_range_B_refined3.908
r_long_range_B_other3.907
r_scangle_other2.704
r_angle_refined_deg1.977
r_mcangle_it1.731
r_mcangle_other1.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.477
r_dihedral_angle_4_deg19.053
r_dihedral_angle_3_deg15.181
r_dihedral_angle_1_deg7.107
r_long_range_B_refined3.908
r_long_range_B_other3.907
r_scangle_other2.704
r_angle_refined_deg1.977
r_mcangle_it1.731
r_mcangle_other1.73
r_scbond_it1.705
r_scbond_other1.705
r_angle_other_deg1.092
r_mcbond_it1.055
r_mcbond_other1.054
r_chiral_restr0.12
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2078
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
MOLREPphasing