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NM-02 in complex with HER2-ECD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MY6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 13% PEG6000 (w/v), 0.1 M MES pH 6.5, 7% 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 3.578768 65.65199
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.767 α = 90 b = 105.767 β = 90 c = 185.882 γ = 120
Symmetry Space Group P 32 2 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 PIXEL DECTRIS PILATUS3 6M 2019-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96872 Diamond I24
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 3.1 65.324 100 0.99 5.1 19.2 22490 101.26
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 3.1 3.31 100 0.34 0.7 19.7
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-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 FREE R-VALUE 5MY6 3.1 65.324 22447 1186 99.858 0.278 0.2747 0.2751 0.2821 0.3299 0.3377 Random selection 105.683
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] -3.441 -1.721 -3.441 11.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.735 r_dihedral_angle_3_deg 17.891 r_dihedral_angle_4_deg 12.787 r_lrange_it 11.966 r_lrange_other 11.966 r_mcangle_it 8.358 r_mcangle_other 8.357 r_scangle_it 7.346 r_scangle_other 7.345 r_dihedral_angle_1_deg 6.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.735 r_dihedral_angle_3_deg 17.891 r_dihedral_angle_4_deg 12.787 r_lrange_it 11.966 r_lrange_other 11.966 r_mcangle_it 8.358 r_mcangle_other 8.357 r_scangle_it 7.346 r_scangle_other 7.345 r_dihedral_angle_1_deg 6.404 r_mcbond_other 5.053 r_mcbond_it 5.052 r_scbond_it 4.345 r_scbond_other 4.345 r_angle_other_deg 2.586 r_angle_refined_deg 1.406 r_symmetry_xyhbond_nbd_refined 0.586 r_symmetry_nbd_other 0.251 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.193 r_nbd_other 0.192 r_nbtor_refined 0.161 r_xyhbond_nbd_other 0.142 r_symmetry_nbd_refined 0.107 r_symmetry_xyhbond_nbd_other 0.082 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.05 r_bond_other_d 0.036 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4783 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing