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Crystal structure of mammalian Rev7 in complex with human Rev3 second binding site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EKL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M sodium formate, 0.1 M ammonium acetate, 0.1 M sodium citrate tribasic
dehydrate, 0.1 M sodium potassium tartrate tetrahydrate, 0.1 M sodium oxamate, 0.1 M Imidazole -
MES monohydrate (acid) pH 6.5 and 12.5% v/v MPD, 12.5% PEG 1000, 12.5% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.01 38.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.2 α = 90 b = 48.64 β = 90 c = 116.81 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 2M 2015-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.97853 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.76 58.4 99.7 0.182 7.5 5.45 5897
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.76 2.95 99.7 0.415 5.14
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 6EKL 2.76 58.4 5820 298 99.5 0.23152 0.23009 0.2237 0.25843 0.2465 RANDOM 55.843
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] -5.09 5.43 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.244 r_dihedral_angle_4_deg 21.538 r_dihedral_angle_3_deg 17.013 r_long_range_B_refined 6.846 r_long_range_B_other 6.844 r_scangle_other 3.752 r_angle_other_deg 3.352 r_mcangle_it 3.33 r_mcangle_other 3.328 r_scbond_it 2.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.244 r_dihedral_angle_4_deg 21.538 r_dihedral_angle_3_deg 17.013 r_long_range_B_refined 6.846 r_long_range_B_other 6.844 r_scangle_other 3.752 r_angle_other_deg 3.352 r_mcangle_it 3.33 r_mcangle_other 3.328 r_scbond_it 2.491 r_scbond_other 2.491 r_mcbond_other 1.932 r_mcbond_it 1.931 r_angle_refined_deg 1.39 r_dihedral_angle_1_deg 1.202 r_chiral_restr 0.095 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1819 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing