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Crystal structure of retroviral protease-like domain of Ddi1 from Toxoplasma gondii
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 293 2 M ammonium citrate tribasic, 30 % 2-propanol
Crystal Properties Matthews coefficient Solvent content 4.68 73.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.601 α = 90 b = 184.601 β = 90 c = 184.338 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS 2M 2019-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.99 ELETTRA 11.2C
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 2.12 65.27 100 0.99 13.9 8.6 176969
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 2.126 2.182 0.365
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2I1A 2.126 65.266 176969 8844 99.688 0.195 0.1922 0.2229 0.2475 0.2734 31.448
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] -8.886 -8.886 17.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.989 r_dihedral_angle_3_deg 21.095 r_dihedral_angle_4_deg 19.911 r_lrange_it 7.732 r_lrange_other 7.732 r_dihedral_angle_1_deg 7.418 r_scangle_it 7.112 r_scangle_other 7.112 r_mcangle_it 6.752 r_mcangle_other 6.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.989 r_dihedral_angle_3_deg 21.095 r_dihedral_angle_4_deg 19.911 r_lrange_it 7.732 r_lrange_other 7.732 r_dihedral_angle_1_deg 7.418 r_scangle_it 7.112 r_scangle_other 7.112 r_mcangle_it 6.752 r_mcangle_other 6.752 r_scbond_it 6.212 r_scbond_other 6.211 r_mcbond_it 5.856 r_mcbond_other 5.85 r_rigid_bond_restr 5.042 r_angle_refined_deg 1.833 r_angle_other_deg 1.464 r_symmetry_nbd_refined 0.652 r_symmetry_xyhbond_nbd_refined 0.606 r_nbd_other 0.535 r_xyhbond_nbd_other 0.444 r_symmetry_nbd_other 0.226 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.18 r_ncsr_local_group_35 0.166 r_ncsr_local_group_27 0.164 r_ncsr_local_group_37 0.16 r_ncsr_local_group_63 0.159 r_ncsr_local_group_22 0.158 r_ncsr_local_group_38 0.158 r_ncsr_local_group_48 0.158 r_ncsr_local_group_13 0.157 r_ncsr_local_group_61 0.157 r_ncsr_local_group_62 0.157 r_ncsr_local_group_8 0.156 r_ncsr_local_group_2 0.155 r_ncsr_local_group_29 0.155 r_ncsr_local_group_42 0.155 r_ncsr_local_group_28 0.154 r_ncsr_local_group_30 0.154 r_ncsr_local_group_36 0.154 r_ncsr_local_group_53 0.154 r_ncsr_local_group_57 0.154 r_ncsr_local_group_31 0.153 r_ncsr_local_group_45 0.153 r_ncsr_local_group_66 0.153 r_ncsr_local_group_34 0.151 r_ncsr_local_group_59 0.151 r_ncsr_local_group_3 0.149 r_ncsr_local_group_7 0.149 r_ncsr_local_group_21 0.149 r_ncsr_local_group_33 0.149 r_ncsr_local_group_60 0.149 r_ncsr_local_group_10 0.148 r_ncsr_local_group_25 0.148 r_ncsr_local_group_44 0.147 r_ncsr_local_group_51 0.147 r_ncsr_local_group_47 0.146 r_ncsr_local_group_11 0.145 r_ncsr_local_group_46 0.145 r_ncsr_local_group_52 0.145 r_ncsr_local_group_54 0.145 r_ncsr_local_group_56 0.145 r_ncsr_local_group_9 0.144 r_ncsr_local_group_32 0.144 r_ncsr_local_group_40 0.144 r_ncsr_local_group_6 0.143 r_ncsr_local_group_12 0.143 r_ncsr_local_group_26 0.142 r_ncsr_local_group_50 0.142 r_ncsr_local_group_16 0.141 r_ncsr_local_group_23 0.141 r_ncsr_local_group_1 0.14 r_ncsr_local_group_18 0.14 r_ncsr_local_group_20 0.14 r_ncsr_local_group_41 0.14 r_ncsr_local_group_49 0.14 r_ncsr_local_group_65 0.14 r_ncsr_local_group_4 0.139 r_ncsr_local_group_58 0.138 r_ncsr_local_group_64 0.137 r_ncsr_local_group_5 0.136 r_ncsr_local_group_14 0.136 r_ncsr_local_group_17 0.135 r_ncsr_local_group_15 0.134 r_ncsr_local_group_43 0.133 r_ncsr_local_group_39 0.131 r_ncsr_local_group_19 0.13 r_ncsr_local_group_55 0.128 r_symmetry_xyhbond_nbd_other 0.126 r_ncsr_local_group_24 0.125 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11178 Nucleic Acid Atoms Solvent Atoms 585 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing