☰ Navigation Tabs
Small peptide enhances the binding of nutline-3a to MdmX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7C3Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 20% v/v Tacsimate pH7.0, 0.1 M HEPES pH7.5, 2% v/v Polythylene glycol 200
Crystal Properties Matthews coefficient Solvent content 2.07 40.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.844 α = 90 b = 47.879 β = 90.053 c = 92.233 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 PIXEL DECTRIS EIGER2 X 16M 2020-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.9792 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.68 47.844 100 0.092 0.094 0.019 1 25.4 23.7 43877
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.71 99.8 1.256 1.289 0.287 0.84 19.9
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 NONE 7C3Y 1.73 47.844 43877 2302 99.952 0.206 0.2045 0.2045 0.241 0.2409 26.721
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] 0.386 -0.07 0.403 -0.789
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.793 r_dihedral_angle_6_deg 16.152 r_dihedral_angle_2_deg 11.9 r_lrange_other 8.499 r_lrange_it 8.494 r_dihedral_angle_1_deg 7.293 r_scangle_it 6.07 r_scangle_other 6.069 r_mcangle_it 4.106 r_mcangle_other 4.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.793 r_dihedral_angle_6_deg 16.152 r_dihedral_angle_2_deg 11.9 r_lrange_other 8.499 r_lrange_it 8.494 r_dihedral_angle_1_deg 7.293 r_scangle_it 6.07 r_scangle_other 6.069 r_mcangle_it 4.106 r_mcangle_other 4.105 r_scbond_it 3.825 r_scbond_other 3.824 r_mcbond_it 2.731 r_mcbond_other 2.716 r_angle_refined_deg 1.572 r_angle_other_deg 0.514 r_symmetry_nbd_refined 0.289 r_nbd_refined 0.248 r_nbd_other 0.227 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.189 r_symmetry_xyhbond_nbd_refined 0.184 r_xyhbond_nbd_refined 0.177 r_ncsr_local_group_6 0.089 r_ncsr_local_group_5 0.087 r_ncsr_local_group_4 0.085 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.078 r_ncsr_local_group_3 0.077 r_ncsr_local_group_2 0.075 r_ncsr_local_group_1 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3140 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 232
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling HKL-3000 data collection MOLREP phasing