2DQK

Crystal structure of the complex of proteinase K with a specific lactoferrin peptide Val-Leu-Leu-His at 1.93 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298sodium nitrate, CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1542.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.313α = 90
b = 68.313β = 90
c = 108.407γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291IMAGE PLATEMAR scanner 345 mm platemirror2006-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

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
11.9357.7498.61988419884
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.931.9699.2

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3PRK1.9357.741988418805101299.190.160.15360.151820.1871RANDOM13.263
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]
-0.16-0.160.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.529
r_dihedral_angle_1_deg3.848
r_scangle_it3.315
r_scbond_it1.931
r_angle_refined_deg1.318
r_mcangle_it0.996
r_mcbond_it0.496
r_symmetry_vdw_refined0.232
r_nbd_refined0.213
r_symmetry_hbond_refined0.161
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.529
r_dihedral_angle_1_deg3.848
r_scangle_it3.315
r_scbond_it1.931
r_angle_refined_deg1.318
r_mcangle_it0.996
r_mcbond_it0.496
r_symmetry_vdw_refined0.232
r_nbd_refined0.213
r_symmetry_hbond_refined0.161
r_xyhbond_nbd_refined0.14
r_chiral_restr0.085
r_metal_ion_refined0.029
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms2064
Nucleic Acid Atoms
Solvent Atoms291
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing