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Crystal structure of Rev7-K44A/R124A/A135D in complex with Rev3-RBM2 (residues 1988-2014)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ABD 3ABD (excluding Rev3 peptide)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.25 289.15 well solution containing 100 mM sodium citrate, 1.6 M ammonium sulfate, pH=5.25 was mixed at 1:1 ratio with protein at 45 mg/mL in 5 mM HEPES, 100 mM NaCl, 10 mM DTT, pH=7.4
Crystal Properties Matthews coefficient Solvent content 2.7 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.58 α = 90 b = 64.58 β = 90 c = 116.547 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 289.15 PIXEL DECTRIS PILATUS3 S 6M 2016-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.976 CHESS F1
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 1.43 116.55 98.5 0.045 0.048 0.016 41.78 9.6 51936
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 3ABD (excluding Rev3 peptide) 1.43 116.55 51936 2521 98.49 0.176 0.1749 0.1831 0.1974 0.2083 RANDOM 29.8026
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] 0.83 0.42 0.83 -2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.145 r_dihedral_angle_4_deg 14.894 r_dihedral_angle_3_deg 14.726 r_dihedral_angle_1_deg 6.821 r_mcangle_it 4.69 r_angle_other_deg 3.679 r_mcbond_it 3.255 r_mcbond_other 3.255 r_angle_refined_deg 2.367 r_chiral_restr 0.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.145 r_dihedral_angle_4_deg 14.894 r_dihedral_angle_3_deg 14.726 r_dihedral_angle_1_deg 6.821 r_mcangle_it 4.69 r_angle_other_deg 3.679 r_mcbond_it 3.255 r_mcbond_other 3.255 r_angle_refined_deg 2.367 r_chiral_restr 0.148 r_gen_planes_other 0.027 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1856 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing Coot model building REFMAC refinement