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Structure of Oligopeptidase B from Leishmania major
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.2 PROTEIN 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 coefficient Solvent content 4.2 71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.478 α = 90 b = 142.776 β = 90 c = 208.919 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 IMAGE PLATE MARRESEARCH MIRRORS 2008-06-10 M SINGLE WAVELENGTH 2 1 x-ray 103 CCD MARRESEARCH M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 2 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.65 32 98.4 0.06 8.8 3.3 167772 1.5 29.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 100 0.46 1.7 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT NONE 1.65 117.851 167169 8321 98.007 0.142 0.1403 0.1459 0.178 0.1822 RANDOM 41.338
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.738 r_dihedral_angle_4_deg 15.532 r_dihedral_angle_3_deg 12.49 r_scangle_it 9.512 r_scbond_it 6.794 r_dihedral_angle_1_deg 6.661 r_mcangle_it 4.118 r_rigid_bond_restr 3.903 r_mcbond_it 2.833 r_angle_refined_deg 2.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.738 r_dihedral_angle_4_deg 15.532 r_dihedral_angle_3_deg 12.49 r_scangle_it 9.512 r_scbond_it 6.794 r_dihedral_angle_1_deg 6.661 r_mcangle_it 4.118 r_rigid_bond_restr 3.903 r_mcbond_it 2.833 r_angle_refined_deg 2.353 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.222 r_symmetry_hbond_refined 0.215 r_chiral_restr 0.209 r_xyhbond_nbd_refined 0.161 r_metal_ion_refined 0.065 r_bond_refined_d 0.035 r_gen_planes_refined 0.014 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 Atoms Number Protein Atoms 5809 Nucleic Acid Atoms Solvent Atoms 721 Heterogen Atoms 326
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction SCALA data scaling autoSHARP phasing SHELXCD phasing SHELXD phasing