5F8T

The crystal structure of human Plasma Kallikrein in complex with its peptide inhibitor pkalin-2


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529825% PEG 3350, 0.1M Hepes, pH 7.5, 20mM (NH4)2SO4
Crystal Properties
Matthews coefficientSolvent content
2.448.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.153α = 90
b = 90.153β = 90
c = 57.26γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2014-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.755099.915.25.527101
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.75

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 REPLACEMENTTHROUGHOUT2ANY1.755025717135899.90.2310.2310.245RANDOM30.21
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]
0.10.050.1-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.347
r_dihedral_angle_3_deg13.456
r_dihedral_angle_4_deg13.394
r_dihedral_angle_1_deg6.069
r_long_range_B_refined5.468
r_long_range_B_other5.249
r_mcangle_it2.484
r_mcangle_other2.483
r_scangle_other2.415
r_scbond_it1.455
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.347
r_dihedral_angle_3_deg13.456
r_dihedral_angle_4_deg13.394
r_dihedral_angle_1_deg6.069
r_long_range_B_refined5.468
r_long_range_B_other5.249
r_mcangle_it2.484
r_mcangle_other2.483
r_scangle_other2.415
r_scbond_it1.455
r_mcbond_it1.435
r_mcbond_other1.433
r_scbond_other1.433
r_angle_refined_deg1.197
r_angle_other_deg0.73
r_chiral_restr0.068
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms1970
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling