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Macrophage Migration Inhibitory Factor 1 from Necator Americanus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298.15 60 %v/v Tacsimate (Precipitant)
Crystal Properties Matthews coefficient Solvent content 3.94 68.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.632 α = 90 b = 126.213 β = 90 c = 155.766 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 100 PIXEL DECTRIS EIGER X 16M 2023-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920105 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.098 98.255 99.9 0.146 0.161 0.995 7.4 5.7 143699
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.098 2.134 100 2.078 2.29 0.345 1 5.7
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.098 98.255 143346 7180 99.695 0.2 0.1976 0.2397 0.2566 43.583
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] 1.013 -1.54 0.527
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.615 r_lrange_other 17.543 r_dihedral_angle_6_deg 16.714 r_scangle_it 14.362 r_scangle_other 14.361 r_dihedral_angle_3_deg 13.5 r_mcangle_it 11.271 r_mcangle_other 11.271 r_scbond_it 10.314 r_scbond_other 10.313
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.615 r_lrange_other 17.543 r_dihedral_angle_6_deg 16.714 r_scangle_it 14.362 r_scangle_other 14.361 r_dihedral_angle_3_deg 13.5 r_mcangle_it 11.271 r_mcangle_other 11.271 r_scbond_it 10.314 r_scbond_other 10.313 r_mcbond_it 8.317 r_mcbond_other 8.312 r_dihedral_angle_2_deg 7.724 r_dihedral_angle_1_deg 5.963 r_rigid_bond_restr 5.304 r_angle_refined_deg 1.686 r_angle_other_deg 0.517 r_nbd_other 0.221 r_nbd_refined 0.208 r_symmetry_nbd_other 0.202 r_symmetry_nbd_refined 0.174 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.142 r_symmetry_xyhbond_nbd_refined 0.127 r_ncsr_local_group_32 0.088 r_ncsr_local_group_31 0.087 r_ncsr_local_group_22 0.086 r_ncsr_local_group_38 0.086 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_35 0.084 r_ncsr_local_group_33 0.083 r_ncsr_local_group_11 0.082 r_ncsr_local_group_5 0.081 r_ncsr_local_group_4 0.08 r_ncsr_local_group_6 0.08 r_ncsr_local_group_8 0.08 r_ncsr_local_group_41 0.08 r_ncsr_local_group_7 0.078 r_ncsr_local_group_60 0.078 r_ncsr_local_group_2 0.077 r_ncsr_local_group_37 0.076 r_ncsr_local_group_15 0.075 r_ncsr_local_group_36 0.075 r_ncsr_local_group_47 0.075 r_ncsr_local_group_13 0.074 r_ncsr_local_group_26 0.074 r_ncsr_local_group_50 0.074 r_ncsr_local_group_57 0.074 r_ncsr_local_group_10 0.071 r_ncsr_local_group_44 0.071 r_ncsr_local_group_52 0.071 r_ncsr_local_group_55 0.071 r_chiral_restr 0.07 r_ncsr_local_group_9 0.07 r_ncsr_local_group_59 0.069 r_ncsr_local_group_66 0.068 r_ncsr_local_group_1 0.066 r_ncsr_local_group_25 0.066 r_ncsr_local_group_29 0.066 r_ncsr_local_group_40 0.066 r_ncsr_local_group_43 0.066 r_ncsr_local_group_46 0.066 r_ncsr_local_group_58 0.066 r_ncsr_local_group_34 0.065 r_ncsr_local_group_62 0.065 r_ncsr_local_group_3 0.064 r_ncsr_local_group_20 0.064 r_ncsr_local_group_48 0.064 r_ncsr_local_group_64 0.064 r_ncsr_local_group_17 0.063 r_ncsr_local_group_24 0.063 r_ncsr_local_group_49 0.063 r_ncsr_local_group_53 0.063 r_ncsr_local_group_56 0.063 r_ncsr_local_group_28 0.062 r_ncsr_local_group_39 0.062 r_ncsr_local_group_16 0.061 r_ncsr_local_group_65 0.06 r_ncsr_local_group_61 0.058 r_ncsr_local_group_12 0.056 r_ncsr_local_group_51 0.054 r_ncsr_local_group_54 0.054 r_ncsr_local_group_18 0.053 r_ncsr_local_group_19 0.053 r_ncsr_local_group_14 0.052 r_ncsr_local_group_21 0.051 r_ncsr_local_group_23 0.051 r_ncsr_local_group_45 0.051 r_ncsr_local_group_42 0.05 r_ncsr_local_group_30 0.041 r_ncsr_local_group_63 0.04 r_ncsr_local_group_27 0.034 r_chiral_restr_other 0.032 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10838 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing