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Crystal structure of human Rev3-Rev7-Rev1-Polkappa complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GK0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 soaking the Rev3-Rev7-Rev1 crystals with the RIR peptide of Polkappa 5.8 289 0.1M sodium citrate, 1.95M sodium formate, 20mM DTT , pH 5.8, soaking the Rev3-Rev7-Rev1 crystals with the RIR peptide of Polkappa, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.36 47.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.998 α = 90 b = 72.762 β = 90 c = 104.653 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 315r 2012-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9795 SSRF BL17U
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 3.2 20 100 0.087 21.5 6.4 14623 14623
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 3.2 3.31 100 0.431 5.2 6.4 1531
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4GK0 3.21 20 14623 14623 770 99.05 0.23408 0.23408 0.23154 0.2275 0.281 0.2686 RANDOM 52.377
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] -3.52 -2.05 5.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.55 r_dihedral_angle_3_deg 20.086 r_dihedral_angle_4_deg 19.503 r_dihedral_angle_1_deg 6.995 r_angle_other_deg 3.487 r_angle_refined_deg 1.615 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.55 r_dihedral_angle_3_deg 20.086 r_dihedral_angle_4_deg 19.503 r_dihedral_angle_1_deg 6.995 r_angle_other_deg 3.487 r_angle_refined_deg 1.615 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 5058 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling