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Crystal structure of human DCAF1 WD40 repeats (Q1250L)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CC9 pdb entry 4cc9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 0.1 M sodium hepes, 0.2 M lithium sulfate, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.81 32.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.888 α = 90 b = 99.422 β = 90 c = 84.9 γ = 90
Symmetry Space Group P 21 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 CCD ADSC QUANTUM 315 2013-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97856 APS 19-ID
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 1.72 48.9 100 0.131 11.4 7.3 67989
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 99.8 0.012 1.9 7.4 3555
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 4cc9 1.72 48 67936 2264 99.88 0.184 0.1828 0.2189 0.193 RANDOM 17.9421
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] 1.92 -1.25 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.048 r_dihedral_angle_4_deg 16.762 r_dihedral_angle_3_deg 12.02 r_dihedral_angle_1_deg 7.093 r_mcangle_it 2.971 r_mcbond_it 2.054 r_mcbond_other 2.05 r_angle_refined_deg 1.683 r_angle_other_deg 0.861 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.048 r_dihedral_angle_4_deg 16.762 r_dihedral_angle_3_deg 12.02 r_dihedral_angle_1_deg 7.093 r_mcangle_it 2.971 r_mcbond_it 2.054 r_mcbond_other 2.05 r_angle_refined_deg 1.683 r_angle_other_deg 0.861 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4609 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 45
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction