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Crystal structure of C. crescentus beta sliding clamp with PEG bound to putative beta-motif tethering region
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TR8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 287 25 % PEG1000, 0.2 M NaCl
and 0.1 M Na/K phosphate
Crystal Properties Matthews coefficient Solvent content 3.02 59.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.724 α = 90 b = 123.527 β = 120.01 c = 85.975 γ = 90
Symmetry Space Group C 1 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 100 PIXEL DECTRIS EIGER X 16M 2015-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9793 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.95 50 99.9 0.069 0.027 27.9 7.6 74116 28.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 100 0.5 0.194 4 7.6
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4TR8 1.95 50 74116 3737 99.75 0.171 0.1857 0.219 0.2267 RANDOM 33
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] 0.52 -0.35 -1.59 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.624 r_dihedral_angle_4_deg 13.628 r_dihedral_angle_3_deg 11.995 r_sphericity_free 11.803 r_dihedral_angle_1_deg 6.623 r_rigid_bond_restr 4.611 r_sphericity_bonded 4.519 r_long_range_B_refined 2.719 r_long_range_B_other 2.695 r_scbond_other 2.604
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.624 r_dihedral_angle_4_deg 13.628 r_dihedral_angle_3_deg 11.995 r_sphericity_free 11.803 r_dihedral_angle_1_deg 6.623 r_rigid_bond_restr 4.611 r_sphericity_bonded 4.519 r_long_range_B_refined 2.719 r_long_range_B_other 2.695 r_scbond_other 2.604 r_scbond_it 2.603 r_mcangle_other 2.599 r_mcangle_it 2.598 r_scangle_other 2.522 r_mcbond_it 2.493 r_mcbond_other 2.491 r_angle_refined_deg 1.5 r_angle_other_deg 0.94 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5660 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing Coot model building