2BDA

Porcine pancreatic elastase complexed with N-acetyl-NPI 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 AcNPI, 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
2.0439.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.507α = 90
b = 57.665β = 90
c = 73.872γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray127CCDMARRESEARCHmirrors2005-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.98SLSX06SA

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
11.819.699.50.08611.13.22047014.9
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)
11.81.91000.462.43.32950

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 REPLACEMENTTHROUGHOUT3EST1.819.62047020439105499.190.1730.1730.1710.212RANDOM17.773
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]
0.72-1.350.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.069
r_dihedral_angle_4_deg22.821
r_dihedral_angle_3_deg13.036
r_scangle_it6.487
r_dihedral_angle_1_deg6.118
r_scbond_it5.56
r_mcangle_it3.603
r_mcbond_it2.662
r_angle_refined_deg1.662
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.069
r_dihedral_angle_4_deg22.821
r_dihedral_angle_3_deg13.036
r_scangle_it6.487
r_dihedral_angle_1_deg6.118
r_scbond_it5.56
r_mcangle_it3.603
r_mcbond_it2.662
r_angle_refined_deg1.662
r_nbtor_refined0.309
r_symmetry_vdw_refined0.283
r_nbd_refined0.207
r_symmetry_hbond_refined0.182
r_xyhbond_nbd_refined0.157
r_chiral_restr0.13
r_metal_ion_refined0.069
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 Atoms120
Heterogen Atoms12

Software

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