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Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 2
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 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.75 α = 90 b = 81.75 β = 90 c = 235.633 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 2015-04-26 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 2.64 52.64 94.4 0.994 11.1 13.3 13467
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 2.64 2.77 0.752
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 2.64 52.64 12784 682 92.91 0.16006 0.15759 0.1644 0.20598 0.2072 RANDOM 46.697
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] 0.77 0.39 0.77 -2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.275 r_dihedral_angle_3_deg 16.774 r_dihedral_angle_4_deg 16.368 r_dihedral_angle_1_deg 8.735 r_long_range_B_refined 7.565 r_long_range_B_other 6.839 r_scangle_other 4.26 r_mcangle_it 3.805 r_mcangle_other 3.804 r_scbond_it 2.873
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.275 r_dihedral_angle_3_deg 16.774 r_dihedral_angle_4_deg 16.368 r_dihedral_angle_1_deg 8.735 r_long_range_B_refined 7.565 r_long_range_B_other 6.839 r_scangle_other 4.26 r_mcangle_it 3.805 r_mcangle_other 3.804 r_scbond_it 2.873 r_scbond_other 2.6 r_mcbond_it 2.29 r_mcbond_other 2.289 r_angle_refined_deg 1.916 r_angle_other_deg 1.339 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2376 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing