2PSX

Crystal Structure of Human Kallikrein 5 in complex with Leupeptin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.629130% PEG-monomethyl ether, 200 mM ammomium sulfate, 100 mM MES,10 mM leupeptin, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.2762.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.219α = 90
b = 67.284β = 94.35
c = 39.916γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2006-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW61.0500MPG/DESY, HAMBURGBW6

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
12.32099.70.08321.85.71474014701126.2
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)
12.32.3494.80.2026.4694

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2BDG2.319.91470114047709950.2440.2210.2210.269RANDOM51.5
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]
-8.4-0.7932.22-23.83
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.4
c_scangle_it3.23
c_mcangle_it2.73
c_scbond_it2.18
c_mcbond_it1.6
c_angle_deg1.2
c_improper_angle_d0.8
c_bond_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1793
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms28

Software

Software
Software NamePurpose
CNSrefinement
LABVIEWdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing