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Crystal structure of Rev7-WT/Rev3 as a monomer under high-salt conditions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BC8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 hRev7/3 at 60 mg/mL in 5 mM HEPES, 100 mM NaCl, 10 mM DTT, pH=7.4 was mixed in a 1:1 ratio with a well solution consisting of 100 mM sodium citrate, 1M LiCl, 7.5% (w/v) PEG6000 at pH=4.75. Crystals were frozen in the reservoir solution with the addition of 20% (w/v) sucrose
Crystal Properties Matthews coefficient Solvent content 2.81 56.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.696 α = 90 b = 89.696 β = 90 c = 284.841 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 77 PIXEL DECTRIS PILATUS3 S 6M 2016-03-03 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) 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 2.8 284.84 99.8 0.044 21.1 9.6 33727
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.85 99.9 0.168 0.946 2.2 9.5
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 6BC8 2.8 284.84 33727 1715 99.75 0.2778 0.2754 0.2745 0.3213 0.3211 RANDOM 94.6819
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] -3.5 -1.75 -3.5 11.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.701 r_dihedral_angle_4_deg 22.302 r_dihedral_angle_3_deg 17.212 r_mcangle_it 11.895 r_mcbond_it 7.657 r_mcbond_other 7.656 r_dihedral_angle_1_deg 7.617 r_angle_other_deg 3.518 r_angle_refined_deg 1.527 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.701 r_dihedral_angle_4_deg 22.302 r_dihedral_angle_3_deg 17.212 r_mcangle_it 11.895 r_mcbond_it 7.657 r_mcbond_other 7.656 r_dihedral_angle_1_deg 7.617 r_angle_other_deg 3.518 r_angle_refined_deg 1.527 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6426 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing DENZO data reduction SCALEPACK data scaling PHASER phasing Coot model building