2BDC

Porcine pancreatic elastase complexed with Asn-Pro-Ile 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, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.0841

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.145α = 90
b = 57.874β = 90
c = 74.529γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray127IMAGE PLATERIGAKU RAXIS IVOSMIC mirrors2005-04-26MSINGLE 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
11.819.5895.80.0334.64.51978312
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)
11.81.993.10.06123.24.52737

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 REPLACEMENTTHROUGHOUT3EST1.819.581978319755102495.350.1790.1790.1770.222RANDOM12.992
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]
0.30.09-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.028
r_dihedral_angle_4_deg20.919
r_dihedral_angle_3_deg12.244
r_dihedral_angle_1_deg5.918
r_scangle_it4.878
r_scbond_it4.081
r_mcangle_it2.785
r_mcbond_it2.033
r_angle_refined_deg1.286
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.028
r_dihedral_angle_4_deg20.919
r_dihedral_angle_3_deg12.244
r_dihedral_angle_1_deg5.918
r_scangle_it4.878
r_scbond_it4.081
r_mcangle_it2.785
r_mcbond_it2.033
r_angle_refined_deg1.286
r_nbtor_refined0.306
r_symmetry_vdw_refined0.239
r_nbd_refined0.199
r_symmetry_hbond_refined0.187
r_metal_ion_refined0.131
r_chiral_restr0.098
r_xyhbond_nbd_refined0.088
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 Atoms124
Heterogen Atoms6

Software

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