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Structure of WDR5:CS-VIP8 crystal after illumination at 405 nm and room temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277.15 10% (w/v) PEG20000, 20% (v/v) PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate
Crystal Properties Matthews coefficient Solvent content 1.83 32.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.03 α = 90 b = 46.9 β = 90 c = 126.32 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 EIGER X 16M 2019-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00 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 1.79 44.01 96.07 0.08507 0.09312 0.03712 0.998 11.32 5.9 25827 21.32
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 1.79 1.859 66.56 0.6186 0.7499 0.4115 0.615 1.44 3.1
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 (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 6IAM 1.79 44.01 24059 1279 96.06 0.16817 0.16581 0.1749 0.21361 0.2217 RANDOM 26.346
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] 0.88 -1.56 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.179 r_dihedral_angle_4_deg 20.354 r_dihedral_angle_3_deg 13.582 r_dihedral_angle_1_deg 7.55 r_long_range_B_refined 5.63 r_long_range_B_other 5.589 r_scangle_other 3.101 r_mcangle_it 2.604 r_mcangle_other 2.603 r_scbond_other 2.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.179 r_dihedral_angle_4_deg 20.354 r_dihedral_angle_3_deg 13.582 r_dihedral_angle_1_deg 7.55 r_long_range_B_refined 5.63 r_long_range_B_other 5.589 r_scangle_other 3.101 r_mcangle_it 2.604 r_mcangle_other 2.603 r_scbond_other 2.011 r_scbond_it 1.995 r_mcbond_it 1.672 r_mcbond_other 1.672 r_angle_refined_deg 1.53 r_angle_other_deg 1.068 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2417 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing