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Mutant PolIV-DNA incoming nucleotide complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IRC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 277 MPD 2%, Sodium Phosphate buffer pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.77 55.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.184 α = 90 b = 56.974 β = 92.9 c = 111.136 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 PIXEL DECTRIS PILATUS 6M-F 2018-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0723 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.44 69.71 99.9 0.057 0.999 14.4 6.6 40567
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.57 99.1 0.755 0.313 0.666 6.7
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 4IRC 2.44 69.71 33768 1788 99.96 0.22227 0.22105 0.237 0.24505 0.2604 RANDOM
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] -1.87 -0.05 -2.81 4.66
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 43.067 r_dihedral_angle_2_deg 33.658 r_dihedral_angle_4_deg 23.32 r_dihedral_angle_3_deg 19.535 r_dihedral_angle_1_deg 7.405 r_rigid_bond_restr 6.359 r_long_range_B_refined 3.704 r_mcangle_it 1.669 r_scbond_it 1.393 r_angle_refined_deg 1.183
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 43.067 r_dihedral_angle_2_deg 33.658 r_dihedral_angle_4_deg 23.32 r_dihedral_angle_3_deg 19.535 r_dihedral_angle_1_deg 7.405 r_rigid_bond_restr 6.359 r_long_range_B_refined 3.704 r_mcangle_it 1.669 r_scbond_it 1.393 r_angle_refined_deg 1.183 r_mcbond_it 0.984 r_chiral_restr 0.042 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5378 Nucleic Acid Atoms 1351 Solvent Atoms 40 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling Coot model building PHASER phasing