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Co-crystal structure of SPOP MATH domain and hamster Pdx1 fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 0.1 M Imidazole-HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG-4000
Crystal Properties Matthews coefficient Solvent content 2.03 39.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.4 α = 89.25 b = 55.17 β = 89.89 c = 58.07 γ = 86.76
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 PILATUS3 X 2M 2015-07-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.03 100 96.4 0.106 8.62 3.54 124076 32906
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.102
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 3IVV 2.03 19.85 32906 1650 97.97 0.18806 0.18414 0.1906 0.26169 0.2662 RANDOM 38.798
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] -0.01 0.01 -0.01 0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.658 r_dihedral_angle_4_deg 16.619 r_dihedral_angle_3_deg 15.881 r_long_range_B_refined 7.893 r_long_range_B_other 7.849 r_dihedral_angle_1_deg 7.717 r_scangle_other 5.284 r_mcangle_it 4.715 r_mcangle_other 4.714 r_scbond_it 3.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.658 r_dihedral_angle_4_deg 16.619 r_dihedral_angle_3_deg 15.881 r_long_range_B_refined 7.893 r_long_range_B_other 7.849 r_dihedral_angle_1_deg 7.717 r_scangle_other 5.284 r_mcangle_it 4.715 r_mcangle_other 4.714 r_scbond_it 3.421 r_scbond_other 3.42 r_mcbond_other 3.167 r_mcbond_it 3.166 r_angle_refined_deg 1.693 r_angle_other_deg 1.003 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 4760 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing