5F8Z

The crystal structure of human Plasma Kallikrein in complex with its peptide inhibitor pkalin-1


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529828% PEG 3350, 0.1M TRIS-HCL PH8.5, 20MM (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
Crystal Properties
Matthews coefficientSolvent content
2.4249.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.279α = 90
b = 90.279β = 90
c = 57.623γ = 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
11.578.1899.414.25.742363

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 REPLACEMENTTHROUGHOUT2ANY1.55040208213299.110.181160.179330.21747RANDOM19.358
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]
0.020.010.02-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.865
r_sphericity_free19.877
r_dihedral_angle_4_deg13.746
r_dihedral_angle_3_deg12.767
r_dihedral_angle_1_deg6.031
r_sphericity_bonded5.125
r_long_range_B_refined2.441
r_long_range_B_other2.441
r_scangle_other1.89
r_scbond_it1.881
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.865
r_sphericity_free19.877
r_dihedral_angle_4_deg13.746
r_dihedral_angle_3_deg12.767
r_dihedral_angle_1_deg6.031
r_sphericity_bonded5.125
r_long_range_B_refined2.441
r_long_range_B_other2.441
r_scangle_other1.89
r_scbond_it1.881
r_scbond_other1.88
r_rigid_bond_restr1.832
r_mcangle_other1.566
r_mcangle_it1.563
r_angle_refined_deg1.413
r_mcbond_it1.35
r_mcbond_other1.335
r_angle_other_deg0.94
r_chiral_restr0.088
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.003
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1966
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling