2BD9

Porcine pancreatic elastase complexed with beta-casomorphin-7 and Arg-Phe at pH 5.0 (50 min soak) and immersed in pH 9 buffer for 28 seconds (2nd pH jump)


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 ARG-PHE (2 MG) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 50 MIN , VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.1342.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.38α = 90
b = 57.59β = 90
c = 74.758γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray127IMAGE PLATERIGAKU RAXIS IVOSMIC mirrors2005-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
11.919.8799.40.06316.13.41794423.2
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)
11.92990.32833.32550

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 REPLACEMENTTHROUGHOUT3EST1.919.87179441791091499.140.1750.1750.1720.226RANDOM33.436
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]
2.62-1.01-1.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.843
r_dihedral_angle_4_deg20.939
r_dihedral_angle_3_deg12.282
r_dihedral_angle_1_deg6.109
r_scangle_it5.41
r_scbond_it4.48
r_mcangle_it2.971
r_mcbond_it2.208
r_angle_refined_deg1.274
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.843
r_dihedral_angle_4_deg20.939
r_dihedral_angle_3_deg12.282
r_dihedral_angle_1_deg6.109
r_scangle_it5.41
r_scbond_it4.48
r_mcangle_it2.971
r_mcbond_it2.208
r_angle_refined_deg1.274
r_nbtor_refined0.303
r_symmetry_vdw_refined0.235
r_symmetry_hbond_refined0.233
r_nbd_refined0.192
r_metal_ion_refined0.143
r_xyhbond_nbd_refined0.131
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1802
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms6

Software

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