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Structure of WWP2 2,3-linker-HECT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Y07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 298 0.1 M MMT (DL-malic acid, MES, Tris-base in molar ratio of 1:2:2) pH 6.0, 25% PEG1500
Crystal Properties Matthews coefficient Solvent content 1.83 32.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.041 α = 90 b = 62.581 β = 90 c = 102.372 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 PILATUS 6M 2016-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.75 50 99.1 0.064 0.071 0.029 8.9 6 10662
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 2.75 2.8 98.6 0.463 0.513 0.216 0.834 5.2 504
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 4Y07 2.75 50 10094 483 99.08 0.229 0.2249 0.2294 0.317 0.3071 RANDOM 87.323
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] -0.72 -5.01 5.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.519 r_dihedral_angle_4_deg 17.645 r_dihedral_angle_3_deg 16.938 r_dihedral_angle_1_deg 6.074 r_angle_refined_deg 1.425 r_angle_other_deg 1.037 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.519 r_dihedral_angle_4_deg 17.645 r_dihedral_angle_3_deg 16.938 r_dihedral_angle_1_deg 6.074 r_angle_refined_deg 1.425 r_angle_other_deg 1.037 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3045 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data reduction REFMAC phasing