☰ Navigation Tabs
Crystal structure of the apo Pex5 peroxisomal cargo receptor from Trypanosoma brucei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CVP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 0.9 M sodium-potassium tartrate tetrahydrate, 20% w/v glycerol, 0.05 M Hepes pH 7.4 after 8 days at 293 K
Crystal Properties Matthews coefficient Solvent content 3.94 68.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 206.545 α = 90 b = 206.545 β = 90 c = 67.867 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2019-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.35 47.89 99.89 0.999 14.68 5.8 44917
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.434 0.52 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 2.35 47.89 42612 2307 99.93 0.20025 0.19777 0.204 0.24605 0.2452 RANDOM 54.254
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] 0.53 0.26 0.53 -1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.309 r_dihedral_angle_4_deg 19.494 r_dihedral_angle_3_deg 19.299 r_long_range_B_other 9.215 r_long_range_B_refined 9.208 r_scangle_other 7.384 r_mcangle_it 6.655 r_mcangle_other 6.654 r_dihedral_angle_1_deg 5.967 r_scbond_it 4.993
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.309 r_dihedral_angle_4_deg 19.494 r_dihedral_angle_3_deg 19.299 r_long_range_B_other 9.215 r_long_range_B_refined 9.208 r_scangle_other 7.384 r_mcangle_it 6.655 r_mcangle_other 6.654 r_dihedral_angle_1_deg 5.967 r_scbond_it 4.993 r_scbond_other 4.992 r_mcbond_it 4.672 r_mcbond_other 4.671 r_angle_refined_deg 1.552 r_angle_other_deg 1.349 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4823 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing