☰ Navigation Tabs
WD repeat containing protein 5 (WDR5)- PER1 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M Tris pH 6.5, 100mM (NH4)2SO4, 30% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.98 37.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.613 α = 90 b = 81.028 β = 90 c = 86.426 γ = 90
Symmetry Space Group P 2 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 2023-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
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 1.7 43.21 99.8 0.032 0.034 0.009 1 34.3 13.2 32122
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 1.7 1.73 99.3 0.569 0.592 0.16 0.99 13.6
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 (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 THROUGHOUT 1.7 40.61 30502 1578 99.74 0.19589 0.19338 0.2082 0.24657 0.2491 RANDOM 36.905
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] 5.84 -5.21 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.363 r_dihedral_angle_2_deg 10.102 r_dihedral_angle_1_deg 8.255 r_long_range_B_refined 6.877 r_long_range_B_other 6.862 r_scangle_other 5.434 r_mcangle_it 3.988 r_mcangle_other 3.987 r_scbond_it 3.759 r_scbond_other 3.757
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.363 r_dihedral_angle_2_deg 10.102 r_dihedral_angle_1_deg 8.255 r_long_range_B_refined 6.877 r_long_range_B_other 6.862 r_scangle_other 5.434 r_mcangle_it 3.988 r_mcangle_other 3.987 r_scbond_it 3.759 r_scbond_other 3.757 r_mcbond_it 3.028 r_mcbond_other 3.022 r_angle_refined_deg 1.398 r_angle_other_deg 0.474 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2403 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction