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Crystal structure of Csm1-Csm4 cassette in complex with pppApA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MUA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 293 0.1 M phosphate-citrate
pH 4.2, 5% PEG3000, 25% 1,2-propanediol, and 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.7 54.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.445 α = 90 b = 156.445 β = 90 c = 186.415 γ = 120
Symmetry Space Group P 65 2 2
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 2018-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 50 100 0.03 24.3 34.8 41953
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69
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 6MUA 2.6 49.43 39795 2104 99.76 0.22572 0.22328 0.2236 0.27097 0.265 RANDOM 80.378
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] -0.45 -0.22 -0.45 1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.3 r_dihedral_angle_4_deg 18.235 r_dihedral_angle_3_deg 17.721 r_long_range_B_other 10.799 r_long_range_B_refined 10.798 r_scangle_other 7.309 r_dihedral_angle_1_deg 7.073 r_mcangle_it 6.644 r_mcangle_other 6.643 r_scbond_other 4.515
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.3 r_dihedral_angle_4_deg 18.235 r_dihedral_angle_3_deg 17.721 r_long_range_B_other 10.799 r_long_range_B_refined 10.798 r_scangle_other 7.309 r_dihedral_angle_1_deg 7.073 r_mcangle_it 6.644 r_mcangle_other 6.643 r_scbond_other 4.515 r_scbond_it 4.483 r_mcbond_it 4.204 r_mcbond_other 4.204 r_angle_refined_deg 1.402 r_angle_other_deg 1.122 r_chiral_restr 0.107 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7723 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing