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Small peptide enhances the binding of nutline-3a to N-terminal domain of 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 0.1M HEPES pH6.0, 1.6M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.21 44.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.08 α = 90 b = 47.08 β = 90 c = 90.45 γ = 90
Symmetry Space Group P 43 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 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) 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 1.93 26.81 98.8 0.068 1 24.1 8075
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 1.93 5.23 1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 1.93 26.81 8056 430 98.629 0.214 0.2101 0.2105 0.2838 0.2829 46.762
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] -0.067 -0.067 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.196 r_dihedral_angle_6_deg 15.55 r_lrange_it 15.242 r_lrange_other 15.142 r_dihedral_angle_2_deg 9.54 r_dihedral_angle_1_deg 7.229 r_scangle_it 7.006 r_scangle_other 7 r_mcangle_other 6.13 r_mcangle_it 6.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.196 r_dihedral_angle_6_deg 15.55 r_lrange_it 15.242 r_lrange_other 15.142 r_dihedral_angle_2_deg 9.54 r_dihedral_angle_1_deg 7.229 r_scangle_it 7.006 r_scangle_other 7 r_mcangle_other 6.13 r_mcangle_it 6.125 r_scbond_it 4.63 r_scbond_other 4.626 r_mcbond_other 4.419 r_mcbond_it 4.413 r_angle_refined_deg 1.454 r_symmetry_nbd_refined 0.543 r_angle_other_deg 0.5 r_nbd_refined 0.327 r_symmetry_nbd_other 0.244 r_symmetry_xyhbond_nbd_refined 0.214 r_nbtor_refined 0.198 r_nbd_other 0.19 r_xyhbond_nbd_refined 0.18 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.077 r_bond_refined_d 0.007 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 767 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement xia2 data scaling xia2 data reduction MrBUMP phasing HKL-3000 data collection PDB_EXTRACT data extraction Aimless data scaling