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Mevo lectin complex with mannotetraose (Man4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6 295 Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25% (w/v) polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 2.9 57.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.21 α = 90 b = 168.3 β = 90 c = 170.249 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 PILATUS 6M 2021-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 96.21 100 0.14 0.99 12.1 12 2231847
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 1.33 0.68
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 THROUGHOUT 7DED 2 85.27 186265 9317 99.946 0.227 0.2259 0.2313 0.2496 0.2527 34.575
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] 3.349 -1.499 -1.851
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.641 r_dihedral_angle_3_deg 11.931 r_dihedral_angle_4_deg 10.217 r_dihedral_angle_1_deg 8.062 r_lrange_it 7.442 r_lrange_other 7.433 r_scangle_it 5.86 r_scangle_other 5.86 r_mcangle_other 4.358 r_mcangle_it 4.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.641 r_dihedral_angle_3_deg 11.931 r_dihedral_angle_4_deg 10.217 r_dihedral_angle_1_deg 8.062 r_lrange_it 7.442 r_lrange_other 7.433 r_scangle_it 5.86 r_scangle_other 5.86 r_mcangle_other 4.358 r_mcangle_it 4.357 r_scbond_it 4.047 r_scbond_other 4.047 r_mcbond_it 3.092 r_mcbond_other 3.088 r_angle_other_deg 2.365 r_angle_refined_deg 1.619 r_nbd_other 0.284 r_symmetry_nbd_refined 0.272 r_symmetry_nbd_other 0.213 r_symmetry_xyhbond_nbd_refined 0.183 r_nbd_refined 0.173 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.079 r_ncsr_local_group_16 0.061 r_ncsr_local_group_15 0.058 r_ncsr_local_group_22 0.057 r_ncsr_local_group_52 0.057 r_ncsr_local_group_67 0.057 r_ncsr_local_group_18 0.056 r_ncsr_local_group_39 0.056 r_ncsr_local_group_20 0.055 r_ncsr_local_group_25 0.055 r_ncsr_local_group_55 0.055 r_ncsr_local_group_23 0.054 r_ncsr_local_group_50 0.054 r_ncsr_local_group_65 0.054 r_ncsr_local_group_46 0.052 r_ncsr_local_group_27 0.051 r_ncsr_local_group_48 0.051 r_ncsr_local_group_78 0.051 r_ncsr_local_group_88 0.051 r_ncsr_local_group_4 0.049 r_ncsr_local_group_37 0.049 r_ncsr_local_group_51 0.049 r_ncsr_local_group_81 0.049 r_ncsr_local_group_1 0.048 r_ncsr_local_group_6 0.048 r_ncsr_local_group_14 0.048 r_ncsr_local_group_29 0.048 r_ncsr_local_group_47 0.048 r_ncsr_local_group_54 0.048 r_ncsr_local_group_66 0.048 r_ncsr_local_group_70 0.048 r_ncsr_local_group_19 0.047 r_ncsr_local_group_41 0.047 r_ncsr_local_group_49 0.047 r_ncsr_local_group_68 0.047 r_ncsr_local_group_79 0.047 r_ncsr_local_group_44 0.046 r_ncsr_local_group_64 0.046 r_ncsr_local_group_21 0.044 r_ncsr_local_group_24 0.044 r_ncsr_local_group_33 0.044 r_ncsr_local_group_86 0.044 r_ncsr_local_group_90 0.044 r_symmetry_xyhbond_nbd_other 0.043 r_ncsr_local_group_42 0.043 r_ncsr_local_group_8 0.042 r_ncsr_local_group_56 0.042 r_ncsr_local_group_69 0.042 r_ncsr_local_group_3 0.041 r_ncsr_local_group_10 0.041 r_ncsr_local_group_13 0.041 r_ncsr_local_group_17 0.041 r_ncsr_local_group_40 0.041 r_ncsr_local_group_85 0.041 r_ncsr_local_group_26 0.04 r_ncsr_local_group_34 0.04 r_ncsr_local_group_36 0.04 r_ncsr_local_group_38 0.04 r_ncsr_local_group_45 0.04 r_ncsr_local_group_77 0.04 r_ncsr_local_group_71 0.039 r_ncsr_local_group_76 0.039 r_ncsr_local_group_53 0.038 r_ncsr_local_group_82 0.038 r_ncsr_local_group_87 0.038 r_ncsr_local_group_43 0.037 r_ncsr_local_group_60 0.037 r_bond_other_d 0.036 r_ncsr_local_group_80 0.036 r_ncsr_local_group_58 0.035 r_ncsr_local_group_73 0.035 r_ncsr_local_group_63 0.034 r_ncsr_local_group_91 0.034 r_ncsr_local_group_83 0.033 r_ncsr_local_group_11 0.032 r_ncsr_local_group_2 0.031 r_ncsr_local_group_61 0.031 r_ncsr_local_group_89 0.03 r_ncsr_local_group_32 0.029 r_ncsr_local_group_74 0.029 r_ncsr_local_group_31 0.028 r_ncsr_local_group_30 0.027 r_ncsr_local_group_5 0.023 r_ncsr_local_group_9 0.023 r_ncsr_local_group_12 0.023 r_ncsr_local_group_35 0.023 r_ncsr_local_group_28 0.022 r_ncsr_local_group_59 0.022 r_ncsr_local_group_84 0.022 r_ncsr_local_group_7 0.018 r_ncsr_local_group_57 0.018 r_ncsr_local_group_72 0.018 r_ncsr_local_group_75 0.018 r_chiral_restr_other 0.016 r_bond_refined_d 0.013 r_gen_planes_other 0.012 r_ncsr_local_group_62 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14899 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 636
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing