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Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.5 293 0.1 M sodium acetate trihydrate, 30 % polyethylene glycol 1500
Crystal Properties Matthews coefficient Solvent content 2.1 41.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.53 α = 90 b = 80.39 β = 90 c = 85.45 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2016-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.25 58.55 96.76 0.136 0.136 0.971 5.9 2.6 22170
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.32 98.7 0.34 0.339 0.324 2.7 2.4
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 MOLECULAR REPLACEMENT THROUGHOUT 2I1A 2.25 42.72 21101 1069 96.76 0.16788 0.1642 0.156 0.23981 0.2252 RANDOM 16.669
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] 1.33 2.12 -3.1 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.146 r_dihedral_angle_3_deg 15.55 r_dihedral_angle_4_deg 14.199 r_dihedral_angle_1_deg 6.873 r_long_range_B_refined 4.967 r_long_range_B_other 4.771 r_mcangle_it 2.341 r_mcangle_other 2.34 r_scangle_other 1.883 r_angle_refined_deg 1.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.146 r_dihedral_angle_3_deg 15.55 r_dihedral_angle_4_deg 14.199 r_dihedral_angle_1_deg 6.873 r_long_range_B_refined 4.967 r_long_range_B_other 4.771 r_mcangle_it 2.341 r_mcangle_other 2.34 r_scangle_other 1.883 r_angle_refined_deg 1.855 r_mcbond_it 1.486 r_mcbond_other 1.479 r_scbond_it 1.215 r_scbond_other 1.215 r_angle_other_deg 1.095 r_chiral_restr 0.098 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 3927 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing