2BDB

Porcine pancreatic elastase complexed with Asn-Pro-Ile and Ala-Ala 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 NPI, AND THEN SOAKED WITH Ala-Ala (2 MG) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 30 MIN, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.0840.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.463α = 90
b = 57.663β = 90
c = 74.233γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray127IMAGE PLATERIGAKU RAXIS IVOSMIC MIRRORS2005-06-16MSINGLE 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
11.717.4699.90.03424.83.62448016.3
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)
11.71.7999.90.1448.23.53493

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 REPLACEMENTTHROUGHOUT3EST1.717.462448024434124599.840.1650.1650.1630.194RANDOM17.222
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]
0.07-0.420.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.705
r_dihedral_angle_4_deg23.958
r_dihedral_angle_3_deg11.371
r_dihedral_angle_1_deg5.673
r_scangle_it5.203
r_scbond_it4.108
r_mcangle_it2.872
r_mcbond_it2.024
r_angle_refined_deg1.371
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.705
r_dihedral_angle_4_deg23.958
r_dihedral_angle_3_deg11.371
r_dihedral_angle_1_deg5.673
r_scangle_it5.203
r_scbond_it4.108
r_mcangle_it2.872
r_mcbond_it2.024
r_angle_refined_deg1.371
r_nbtor_refined0.307
r_symmetry_vdw_refined0.222
r_nbd_refined0.202
r_symmetry_hbond_refined0.166
r_xyhbond_nbd_refined0.116
r_chiral_restr0.109
r_metal_ion_refined0.104
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1802
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms17

Software

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