2XE4

Structure of Oligopeptidase B from Leishmania major


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.2PROTEIN WAS DIALYZED INTO 50 MM TRIS, PH 8.0 AND INCUBATED WITH 10 MM ANTIPAIN FOR 30 MINS. THIS WAS MIXED IN A 1:1 RATIO WITH 25% 1,2 PROPANEDIOL, 10% GLYCEROL, 5 % PEG300 AND 0.1 M PHOSPHATE CITRATE, PH 4.2
Crystal Properties
Matthews coefficientSolvent content
4.271

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.478α = 90
b = 142.776β = 90
c = 208.919γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103IMAGE PLATEMARRESEARCHMIRRORS2008-06-10MSINGLE WAVELENGTH
21x-ray103CCDMARRESEARCHM
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007
2SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.653298.40.068.83.31677721.529.5
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)
11.651.711000.461.73

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUTNONE1.65117.851167169832198.0070.1420.14030.178RANDOM41.338
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]
2.673-1.71-0.963
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.738
r_dihedral_angle_4_deg15.532
r_dihedral_angle_3_deg12.49
r_scangle_it9.512
r_scbond_it6.794
r_dihedral_angle_1_deg6.661
r_mcangle_it4.118
r_rigid_bond_restr3.903
r_mcbond_it2.833
r_angle_refined_deg2.353
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.738
r_dihedral_angle_4_deg15.532
r_dihedral_angle_3_deg12.49
r_scangle_it9.512
r_scbond_it6.794
r_dihedral_angle_1_deg6.661
r_mcangle_it4.118
r_rigid_bond_restr3.903
r_mcbond_it2.833
r_angle_refined_deg2.353
r_nbtor_refined0.304
r_symmetry_vdw_refined0.227
r_nbd_refined0.222
r_symmetry_hbond_refined0.215
r_chiral_restr0.209
r_xyhbond_nbd_refined0.161
r_metal_ion_refined0.065
r_bond_refined_d0.035
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5809
Nucleic Acid Atoms
Solvent Atoms721
Heterogen Atoms326

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
SCALAdata scaling
autoSHARPphasing
SHELXCDphasing
SHELXDphasing