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X-ray structure of Trichomonas vaginalis inactive mutant hydrogenosomal processing peptidase heterodimer (HPPin)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HR6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2 M sodium chloride,
0.1 M sodium cacodylate [pH 6.0],
2.0 M ammonium sulfate
0.2 mM n-dodecylmaltoside
Crystal Properties Matthews coefficient Solvent content 3.35 63.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.91 α = 90 b = 115.1 β = 90 c = 125.115 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD RAYONIX MX-225 2014-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.84 125.11 99.8 0.13 0.147 0.067 0.995 12 4.5 30574
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.84 2.99 99.9 0.905 1.021 0.467 0.649 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT THROUGHOUT 2.84 48 29064 1456 99.7 0.20635 0.20301 0.2032 0.27324 0.2735 RANDOM 58.327
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] 0.04 -0.19 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.125 r_dihedral_angle_3_deg 19.181 r_dihedral_angle_4_deg 17.162 r_long_range_B_refined 8.906 r_dihedral_angle_1_deg 6.507 r_mcangle_it 4.997 r_scbond_it 3.573 r_mcbond_it 3.13 r_angle_refined_deg 1.517 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.125 r_dihedral_angle_3_deg 19.181 r_dihedral_angle_4_deg 17.162 r_long_range_B_refined 8.906 r_dihedral_angle_1_deg 6.507 r_mcangle_it 4.997 r_scbond_it 3.573 r_mcbond_it 3.13 r_angle_refined_deg 1.517 r_chiral_restr 0.107 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6355 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHENIX phasing