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Structural basis of human clamp sliding on DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 11% PEG 3350
0.1M Sodium acetate ph 4.5
Crystal Properties Matthews coefficient Solvent content 2.59 52.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.189 α = 90 b = 180.189 β = 90 c = 76.832 γ = 120
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 EIGER X 4M 2015-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.82 90.09 99.6 0.093 7.3 3.1 22331
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.82 2.97 99.8 0.44 1.7 3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4D2G 2.82 90.09 21184 1134 99.59 0.24846 0.24657 0.2838 0.2598 RANDOM 64.618
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] 0.15 0.08 0.15 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.119 r_dihedral_angle_4_deg 20.404 r_dihedral_angle_3_deg 18.274 r_long_range_B_refined 10.16 r_long_range_B_other 10.143 r_dihedral_angle_1_deg 7.147 r_mcangle_it 5.743 r_mcangle_other 5.742 r_scangle_other 5.687 r_mcbond_other 3.604
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.119 r_dihedral_angle_4_deg 20.404 r_dihedral_angle_3_deg 18.274 r_long_range_B_refined 10.16 r_long_range_B_other 10.143 r_dihedral_angle_1_deg 7.147 r_mcangle_it 5.743 r_mcangle_other 5.742 r_scangle_other 5.687 r_mcbond_other 3.604 r_mcbond_it 3.603 r_scbond_it 3.584 r_scbond_other 3.571 r_angle_refined_deg 1.818 r_angle_other_deg 1.455 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.006 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 5293 Nucleic Acid Atoms 410 Solvent Atoms 40 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing