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Structure of human Rev1-DNA-dNTP ternary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AQ4 PDB entry 2AQ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 20% PEG MME 5000, 400mM Sodium malonate pH 4.6, 100mM Ammonium sulfate, 200mM Sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.44 49.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.436 α = 90 b = 172.78 β = 90.65 c = 129.192 γ = 90
Symmetry Space Group P 1 21 1
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 315 Cryogenically cooled double crystal monochromator with horizontal focusing sagitally bent second mono crystal with 4:1 magnification ratio and vertically focusing mirror 2006-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0000 NSLS X29A
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 2.5 43.07 94.7 0.059 27.4 3.3 72489
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 2.5 2.59 91.6 0.462 2.9375 3.1
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 PDB entry 2AQ4 2.5 43.07 72489 8037 94.39 0.2189 0.21353 0.2055 0.26709 0.2561 RANDOM 41.853
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] -0.44 -1.14 2.77 -2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.872 r_dihedral_angle_3_deg 18.682 r_dihedral_angle_4_deg 17.436 r_dihedral_angle_1_deg 5.326 r_scangle_it 2.113 r_angle_refined_deg 1.343 r_scbond_it 1.321 r_mcangle_it 0.998 r_mcbond_it 0.581 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.872 r_dihedral_angle_3_deg 18.682 r_dihedral_angle_4_deg 17.436 r_dihedral_angle_1_deg 5.326 r_scangle_it 2.113 r_angle_refined_deg 1.343 r_scbond_it 1.321 r_mcangle_it 0.998 r_mcbond_it 0.581 r_nbtor_refined 0.303 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.153 r_symmetry_hbond_refined 0.152 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13025 Nucleic Acid Atoms 2276 Solvent Atoms 96 Heterogen Atoms 125
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling