2BD5

Porcine pancreatic elastase complexed with beta-casomorphin-7 and Lys-Ser at pH 5 and immersed in pH 9 buffer for 30 seconds


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EST 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529425MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND 17.5 MG/ML BCM7, AND THEN SOAKED WITH LYS-SER (50 MG/ML) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 60 MIN , VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.0339.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.655α = 90
b = 57.585β = 90
c = 74.524γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray127IMAGE PLATERIGAKU RAXIS IVOSMIC mirrors2005-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54180

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
11.819.799.90.04620.33.42083721.7
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)
11.81.91000.1815.13.32972

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 REPLACEMENTTHROUGHOUT3EST1.819.72083720794106899.880.1760.1760.1740.212RANDOM30.249
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]
4.23-2.86-1.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.953
r_dihedral_angle_4_deg23.184
r_dihedral_angle_3_deg11.635
r_scangle_it6.714
r_dihedral_angle_1_deg6.462
r_scbond_it5.363
r_mcangle_it3.778
r_mcbond_it2.987
r_angle_refined_deg1.746
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.953
r_dihedral_angle_4_deg23.184
r_dihedral_angle_3_deg11.635
r_scangle_it6.714
r_dihedral_angle_1_deg6.462
r_scbond_it5.363
r_mcangle_it3.778
r_mcbond_it2.987
r_angle_refined_deg1.746
r_nbtor_refined0.312
r_symmetry_vdw_refined0.255
r_symmetry_hbond_refined0.22
r_nbd_refined0.211
r_chiral_restr0.132
r_xyhbond_nbd_refined0.132
r_metal_ion_refined0.109
r_bond_refined_d0.019
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1810
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms11

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling