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Crystal Structure of mitochondrial single-stranded DNA binding proteins from S. cerevisiae, Rim1 (Form1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CQO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 295 0.2 M MgCl2 and 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.5 α = 90 b = 153.14 β = 90 c = 118.61 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS RDI CMOS_8M 2016-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 0.97845 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.8 76.57 100 0.18 0.05 0.997 12 7.4 12631
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 2.8 2.873 1.967 0.527 0.527
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 6CQO 2.8 76.57 11992 617 99.73 0.24729 0.24574 0.25 0.27854 0.2753 RANDOM 77.62
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] 7.13 -3.81 -3.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.489 r_dihedral_angle_3_deg 19.641 r_dihedral_angle_4_deg 13.445 r_long_range_B_refined 8.927 r_long_range_B_other 8.926 r_dihedral_angle_1_deg 7.705 r_scangle_other 6.115 r_mcangle_other 5.582 r_mcangle_it 5.58 r_scbond_it 3.737
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.489 r_dihedral_angle_3_deg 19.641 r_dihedral_angle_4_deg 13.445 r_long_range_B_refined 8.927 r_long_range_B_other 8.926 r_dihedral_angle_1_deg 7.705 r_scangle_other 6.115 r_mcangle_other 5.582 r_mcangle_it 5.58 r_scbond_it 3.737 r_scbond_other 3.737 r_angle_other_deg 3.694 r_mcbond_it 3.49 r_mcbond_other 3.48 r_angle_refined_deg 1.846 r_chiral_restr 0.104 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_gen_planes_other 0.009 r_bond_other_d 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 2896 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing