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Crystal structure of K. lactis Ddc2 N-terminus in complex with S. cerevisiae Rfa1 (K45E mutant) N-OB domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OMB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M lithium sulfate monohydrate, 0.1 M Bis-Tris, 25% PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.46 49.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.42 α = 90 b = 94.59 β = 90 c = 170.84 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 6M 2015-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99999 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.38 50 92.1 0.139 0.993 5.87 3.77 21408 56.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.38 2.45 69.9 0.919 0.355 0.99 2.92
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 5OMB 2.38 47.29 21407 1071 91.75 0.2036 0.2006 0.2161 0.2611 0.2746 RANDOM 57.13
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] -1.5581 -1.3067 2.8647
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.64 t_omega_torsion 2.83 t_angle_deg 1.13 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.64 t_omega_torsion 2.83 t_angle_deg 1.13 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3578 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 3
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing