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Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PXW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M MES pH6.5, 2.13M Lithium acetate
Crystal Properties Matthews coefficient Solvent content 2.75 55.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.924 α = 90 b = 81.924 β = 90 c = 236.778 γ = 120
Symmetry Space Group P 61 2 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 PILATUS 6M 2015-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
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 2.2 52.819 100 0.999 23.3 12.7 24830
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 2.2 2.32 0.932
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 FREE R-VALUE 2.2 52.819 24830 1170 99.98 0.199 0.1968 0.1973 0.2354 0.2372 49.263
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] 0.287 0.144 0.287 -0.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.85 r_dihedral_angle_4_deg 22.827 r_dihedral_angle_3_deg 17.773 r_dihedral_angle_1_deg 9.689 r_lrange_it 8.286 r_lrange_other 8.192 r_scangle_it 4.848 r_scangle_other 4.662 r_mcangle_it 3.922 r_mcangle_other 3.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.85 r_dihedral_angle_4_deg 22.827 r_dihedral_angle_3_deg 17.773 r_dihedral_angle_1_deg 9.689 r_lrange_it 8.286 r_lrange_other 8.192 r_scangle_it 4.848 r_scangle_other 4.662 r_mcangle_it 3.922 r_mcangle_other 3.922 r_scbond_it 3.049 r_scbond_other 2.92 r_mcbond_other 2.531 r_mcbond_it 2.529 r_angle_refined_deg 1.962 r_angle_other_deg 1.377 r_symmetry_nbd_refined 0.348 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.193 r_nbd_other 0.186 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.116 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.066 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2348 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing