2BD2

Porcine pancreatic elastase complexed with beta-casomorphin-7 and Arg-Phe at pH 5.0


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 (2MG) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 45 MIN, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.0239.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.195α = 90
b = 57.883β = 90
c = 74.605γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray127IMAGE PLATERIGAKU RAXIS IVOSMIC mirrors2005-06-30MSINGLE 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
11.719.699.90.03922.93.42454115.98
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)
11.71.791000.1377.73.33510

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 REPLACEMENTTHROUGHOUT3EST1.719.592454124499125299.830.170.170.1680.205RANDOM20.974
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]
0.28-0.08-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.553
r_dihedral_angle_4_deg25.58
r_dihedral_angle_3_deg11.537
r_dihedral_angle_1_deg5.749
r_scangle_it5.505
r_scbond_it4.468
r_mcangle_it3.236
r_mcbond_it2.445
r_angle_refined_deg1.593
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.553
r_dihedral_angle_4_deg25.58
r_dihedral_angle_3_deg11.537
r_dihedral_angle_1_deg5.749
r_scangle_it5.505
r_scbond_it4.468
r_mcangle_it3.236
r_mcbond_it2.445
r_angle_refined_deg1.593
r_nbtor_refined0.311
r_symmetry_vdw_refined0.249
r_symmetry_hbond_refined0.218
r_nbd_refined0.209
r_chiral_restr0.13
r_xyhbond_nbd_refined0.126
r_metal_ion_refined0.122
r_bond_refined_d0.017
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1810
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms13

Software

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