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Crystal structure of a Dna2 peptide in complex with Rpa 70N
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 50 mM Tris-HCl, 35 % PEG 1500, 2 mM TCEP, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.303 α = 90 b = 50.882 β = 103.94 c = 76.528 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 CCD ADSC QUANTUM 315r 2013-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.987 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.5 60 84.3 0.074 0.091 0.051 16.7 2.7 67556
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 79.7 0.801 0.97 0.541 0.525 2.7 6342
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 2B29 1.55 30 57455 1815 81.14 0.2327 0.2316 0.2332 0.2667 0.2686 RANDOM 19.703
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] 0.16 0.19 -0.09 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.475 r_dihedral_angle_3_deg 15.291 r_dihedral_angle_4_deg 14.545 r_dihedral_angle_1_deg 5.757 r_mcangle_it 4.035 r_scbond_it 3.999 r_mcbond_it 2.624 r_angle_refined_deg 1.329 r_chiral_restr 0.081 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.475 r_dihedral_angle_3_deg 15.291 r_dihedral_angle_4_deg 14.545 r_dihedral_angle_1_deg 5.757 r_mcangle_it 4.035 r_scbond_it 3.999 r_mcbond_it 2.624 r_angle_refined_deg 1.329 r_chiral_restr 0.081 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3933 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing