1P7V | pdb_00001p7v

Structure of a complex formed between Proteinase K and a designed heptapeptide inhibitor Pro-Ala-Pro-Phe-Ala-Ala-Ala at atomic resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IC6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Microgravity with APCF reactors6.5295tris HCl, CaCl2, NaNO3, pH 6.5, Microgravity with APCF reactors, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9737.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.72α = 90
b = 67.72β = 90
c = 101.62γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATEMARRESEARCHmirrors2000-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.91EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.082099.50.0472815.32101462101462-3-34.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.081.12990.2345.6111322

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-Work (Depositor)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1c61.0820101462101599.650.119940.119740.13993RANDOM7.213
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]
-0.02-0.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.295
r_scangle_it2.998
r_sphericity_free2.615
r_scbond_it1.965
r_sphericity_bonded1.851
r_angle_refined_deg1.411
r_mcangle_it1.336
r_angle_other_deg1.017
r_rigid_bond_restr0.882
r_mcbond_it0.814
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.295
r_scangle_it2.998
r_sphericity_free2.615
r_scbond_it1.965
r_sphericity_bonded1.851
r_angle_refined_deg1.411
r_mcangle_it1.336
r_angle_other_deg1.017
r_rigid_bond_restr0.882
r_mcbond_it0.814
r_symmetry_vdw_other0.307
r_nbd_other0.258
r_nbd_refined0.243
r_symmetry_hbond_refined0.23
r_symmetry_vdw_refined0.211
r_xyhbond_nbd_refined0.16
r_chiral_restr0.132
r_nbtor_other0.086
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4035
Nucleic Acid Atoms
Solvent Atoms452
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing